Psyllid ID: psy9180

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-
Protein Sequence
MGNLASIIGELEELFYINCKNNNNIEQLEEKEEVHLSLRRSKLLMNYVAKVRASPFNPVQKVLFSQNLTPYNFTTNKPKPLLSRFQSLPSFPNLISSSDMAPYVRTVPPWSSPSPPVDLSLGKDRKNDTPSVAFQQLFAGVINSKYANYTICYTDGSKTMNTTSCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQLKLCSPEDFKPIAASIVKKEWQNQWDNVPNTNKLKAIKPLIAPWNTSNQENRTQEIQIKQCEIPASTSLTGYANIYNIPPIPCLIDHVIHSIHGIPTKSEVIIELFSEVLLSKLHNSGVVESRSYTKVLLLTEFVPIMTELVPILTDPTHRSYTQVLLLTEFVPIMTEFVPILTDPTHRYRYLPILTELVPILTVGFGYTRAGQVPNSDTFGILS
Secondary Structure (PSIPRED)
ccccccHHHcccEEEEEccccccHHHHHHHcccccHHHHHHHHHHHHHHHHHcccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccccEEEEEccccccccccEEEEEccccEEEEccccccccHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHHccccccHHHHHHHHHHHHHHcccEEEEEEEccccccccccHHHHHHHcccccccccccccccccHHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccccEEEcccccHHHHHHHHHHHHHHHHccccccccccccccEEEEEEEccccHHcccccccccccccEEEEEEEccccccccccccccccccccEEEEccccccccEEEEEccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHEEEccccccHHHHHHHcccccccHHHHHHHHHHHHHHHccccccHHHHHHHHHHccccccccccccHHHHHHHccccccccccHccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccEEEEEccccccccEEEEEEEEcccEEEcccccccHHHHHHHHHHHHHHHHHHcccccEEEEEccHHHHHHHHccccccHHHHHHHHHHHHHHHcccEEEEEEEcccccccccHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccEEccccccccccccccccccHHEEcccccHHHHHHHccccccccccccccccccEEEHHcccccHHHHHHHHHHHHHHHHHHccccEEcccHHHHEEHHHHcHHHHcccccccccccccHHHHHHHHcccccHHccccccccccccHcHcHHHHcccHEEEEcccccccccccccccccccc
Coil and Loop (DISEMBL)
MGNLASIIGELEELFYINCknnnnieqLEEKEEVHLSLRRSKLLMNYVAKvraspfnpvqkvlfsqnltpynfttnkpkpllsrfqslpsfpnlisssdmapyvrtvppwsspsppvdlslgkdrkndtpsVAFQQLFAGVInskyanyticytdgsktmnttscafsiddlisssqlnpvnsiFSAELIAIYLCLEAitvhpsdqfliVSDSRSALAALSnvsftnplvskvYSCWDLlrsrnkvvhflwcpshcgirgneavdeaarnpvnptqlklcspedfkPIAASIVKKEwqnqwdnvpntnklkaikpliapwntsnqenRTQEIQIkqceipastsltgyaniynippipclidhvihsihgiptKSEVIIELFSEVLLSKLhnsgvvesrsYTKVLLLTEFVpimtelvpiltdpthrsYTQVLLLTEfvpimtefvpiltdpthryrylpiltelvpiltvgfgytragqvpnsdtfgils
Flexible Loop (DISEMBL)
MGNLASIIGELEELFYINCKNNNNIEQLEEKEEVHLSLRRSKLLMNYVAKVRASPFNPVQKVLFSQNLTPYNFTTNKPKPLLSRFQSLPSFPNLISSSDMAPYVRTVPPWSSPSPPVDLSLGKDRKNDTPSVAFQQLFAGVINSKYANYTICYTDGSKTMNTTSCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSnvsftnplVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNptqlklcspeDFKPIAASIVKkewqnqwdnvpntnKLKAIKPLIAPWNTSNQENRTQEIQIKQCEIPASTSLTGYANIYNIPPIPCLIDHVIHSIHGIPTKSEVIIELFSEVLLSKLhnsgvvesrsyTKVLLLTEFVPIMTelvpiltdpthRSYTQVLLLTEFVPIMTEFVPILTDPTHRYRYLPILTELVPILTVGFGytragqvpnsdtfgils
Low Complexity Region (SEG)
MGNLASIIGELEELFYINCKNNNNIEQLEEKEEVHLSLRRSKLLMNYVAKVRASPFNPVQKVLFSQNLTPYNFTTNKPKPLLSRFQSLPSFPNLISSSDMAPYVRTVppwsspsppVDLSLGKDRKNDTPSVAFQQLFAGVINSKYANYTICYTDGSKTMNTTSCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQLKLCSPEDFKPIAASIVKKEWQNQWDNVPNTNKLKAIKPLIAPWNTSNQENRTQEIQIKQCEIPASTSLTGYANIYNIPPIPCLIDHVIHSIHGIPTKSEVIIELFSEVLLSKLHNSGVVESRSYTKVLLLTEFVPIMTELVPILTDPTHRSYTQVLLLTEFVPIMTEFVPILTDPTHRYRYLPILTELVPILTVGFGYTRAGQVPNSDTFGILS
Disordered region (IsUnstruct)
****ASIIGELEELFYINCKNNNNIEQLEEKEEVHLSLRRSKLLMNYVAKVRASPFNPVQKVLFSQNLTPYNFTTN*******************************************************VAFQQLFAGVINSKYANYTICYTDGSKTMNTTSCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDE********TQLKLCSPEDFKPIAASIVKKEWQNQWDNVPNTNKLKAIKPLIAPWNT*******QEIQIKQCEIPASTSLTGYANIYNIPPIPCLIDHVIHSIHGIPTKSEVIIELFSEVLLSKLHNSGVVESRSYTKVLLLTEFVPIMTELVPILTDPTHRSYTQVLLLTEFVPIMTEFVPILTDPTHRYRYLPILTELVPILTVGFGYTRAGQV**********
Disordered Region (DISOPRED)
**NLASIIGELEELFYINCKNNNNIEQLEEKEEVHLSLRRSKLLMNYVAKVRASPFNPVQKVLFSQNLTP**F**NKPKPLLSRFQSLPSFPNLISSSDMAPYVRTVPPWSSPSPPVDLSLGKDRKNDTPSVAFQQLFAGVINSKYANYTICYTDGSKTMNTTSCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQLKLCSPEDFKPIAASIVKKEWQNQWDNVPNTNKLKAIKPLIAPWNTSNQENRTQEIQIKQCEIPASTSLTGYANIYNIPPIPCLIDHVIHSIHGIPTKSEVIIELFSEVLLSKLHNSGVVESRSYTKVLLLTEFVPIMTELVPILTDPTHRSYTQVLLLTEFVPIMTEFVPILTDPTHRYRYLPILTELVPILTVGFGYTRAGQVPNS*TFGILS
Disordered Region (DISEMBL)
MGNLASIIGELEELFYINCKNNNNIEQLEEKEEVHLSLRRSKLLMNYVAKVRASPFNPVQKVLFSQNLTPYNFTTNKPKPLLSRFQSLPSFPNLISSSDMAPYVRTVPPWSSPSPPVDLSLGKDRKNDTPSVAFQQLFAGVINSKYANYTICYTDGSKTMNTTSCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQLKLCSPEDFKPIAASIVKKEWQNQWDNVPNTNKLKAIKPLIAPWNTSNQENRTQEIQIKQCEIPASTSLTGYANIYNIPPIPCLIDHVIHSIHGIPTKSEVIIELFSEVLLSKLHNSGVVESRSYTKVLLLTEFVPIMTELVPILTDPTHRSYTQVLLLTEFVPIMTEFVPILTDPTHRYRYLPILTELVPILTVGFGYTRAGQVPNSDTFGILS
Disordered Region (DISPRO)
*GNLASIIGELEELFYINCKNNNNIEQLEEKEEVHLSLRRSKLLMNYVAKVRASPFNPVQKVLFSQNLTPYNFTTNKPKPLLSRFQSLPSFPNLISSSDMAPYVRTVPPWSSPSPPVDLSLGKDRKNDTPSVAFQQLFAGVINSKYANYTICYTDGSKTMNTTSCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQLKLCSPEDFKPIAASIVKKEWQNQWDNVPNTNKLKAIKPLIAPWNTSNQENRTQEIQIKQCEIPASTSLTGYANIYNIPPIPCLIDHVIHSIHGIPTKSEVIIELFSEVLLSKLHNSGVVESRSYTKVLLLTEFVPIMTELVPILTDPTHRSYTQVLLLTEFVPIMTEFVPILTDPTHRYRYLPILTELVPILTVGFGYTRAGQVPNSD****L*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHoooooooHHHHHHHHHHHHHHHHHHHHHiiiiiiiHHHHHHHHHHHHHHHHooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGNLASIIGELEELFYINCKNNNNIEQLEEKEEVHLSLRRSKLLMNYVAKVRASPFNPVQKVLFSQNLTPYNFTTNKPKPLLSRFQSLPSFPNLISSSDMAPYVRTVPPWSSPSPPVDLSLGKDRKNDTPSVAFQQLFAGVINSKYANYTICYTDGSKTMNTTSCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQLKLCSPEDFKPIAASIVKKEWQNQWDNVPNTNKLKAIKPLIAPWNTSNQENRTQEIQIKQCEIPASTSLTGYANIYNIPPIPCLIDHVIHSIHGIPTKSEVIIELFSEVLLSKLHNSGVVESRSYTKVLLLTEFVPIMTELVPILTDPTHRSYTQVLLLTEFVPIMTEFVPILTDPTHRYRYLPILTELVPILTVGFGYTRAGQVPNSDTFGILS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	491	2.2.26 [Sep-21-2011]
P03371	1145	Pol polyprotein OS=Equine	yes	N/A	0.224	0.096	0.3	0.0003
P32542	1146	Pol polyprotein OS=Equine	yes	N/A	0.224	0.095	0.3	0.0005
P11204	1146	Pol polyprotein OS=Equine	yes	N/A	0.224	0.095	0.3	0.0005

>sp|P03371|POL_EIAVY Pol polyprotein OS=Equine infectious anemia virus (strain Wyoming) GN=pol PE=3 SV=1

 Score = 47.0 bits (110), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 36/120 (30%), Positives = 54/120 (45%), Gaps = 10/120 (8%)

Query: 153 YTDGSKTMNTTSCAF-SIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVS 211
           YTDG K       A+ + +      +L PV     AE +AI + LE        Q  IV+
Sbjct: 623 YTDGGKQNGEGIAAYVTSNGRTKQKRLGPVTHQV-AERMAIQMALEDTR---DKQVNIVT 678

Query: 212 DSRSALAALSNVSFTNPLVSKVYSCWDLLRS--RNKVVHFLWCPSHCGIRGNEAVDEAAR 269
           DS        N++    L       W ++++    ++V+F W P H GI GN+  DEAA+
Sbjct: 679 DS---YYCWKNITEGLGLEGPQNPWWPIIQNIREKEIVYFAWVPGHKGIYGNQLADEAAK 735

During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse transcriptase.
Equus caballus (taxid: 9796)
EC: 3EC: .EC: 1EC: .EC: 1EC: 3EC: .EC: 2

>sp|P32542|POL_EIAVC Pol polyprotein OS=Equine infectious anemia virus (isolate CL22) GN=pol PE=1 SV=1

 Score = 46.2 bits (108), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 36/120 (30%), Positives = 54/120 (45%), Gaps = 10/120 (8%)

Query: 153 YTDGSKTMNTTSCAF-SIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVS 211
           YTDG K       A+ + +      +L PV     AE +AI + LE        Q  IV+
Sbjct: 624 YTDGGKQNGEGIAAYVTSNGRTKQKRLGPVTHQV-AERMAIQMALEDTR---DKQVNIVT 679

Query: 212 DSRSALAALSNVSFTNPLVSKVYSCWDLLRS--RNKVVHFLWCPSHCGIRGNEAVDEAAR 269
           DS        N++    L       W ++++    ++V+F W P H GI GN+  DEAA+
Sbjct: 680 DS---YYCWKNITEGLGLEGPQSPWWPIIQNIREKEIVYFAWVPGHKGICGNQLADEAAK 736

During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse transcriptase.

Equus caballus (taxid: 9796)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: 2

>sp|P11204|POL_EIAV9 Pol polyprotein OS=Equine infectious anemia virus (isolate 1369) GN=pol PE=1 SV=1

 Score = 46.2 bits (108), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 36/120 (30%), Positives = 54/120 (45%), Gaps = 10/120 (8%)

Query: 153 YTDGSKTMNTTSCAF-SIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVS 211
           YTDG K       A+ + +      +L PV     AE +AI + LE        Q  IV+
Sbjct: 624 YTDGGKQNGEGIAAYVTSNGRTKQKRLGPVTHQV-AERMAIQMALEDTR---DKQVNIVT 679

Query: 212 DSRSALAALSNVSFTNPLVSKVYSCWDLLRS--RNKVVHFLWCPSHCGIRGNEAVDEAAR 269
           DS        N++    L       W ++++    ++V+F W P H GI GN+  DEAA+
Sbjct: 680 DS---YYCWKNITEGLGLEGPQSPWWPIIQNIREKEIVYFAWVPGHKGICGNQLADEAAK 736

During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse transcriptase.

Equus caballus (taxid: 9796)

EC: 3

EC: .

EC: 1

EC: .

EC: 1

EC: 3

EC: .

EC: 2

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	491
443693558	502	hypothetical protein CAPTEDRAFT_189741,	0.572	0.559	0.386	4e-36
443695973	261	hypothetical protein CAPTEDRAFT_23017, p	0.492	0.927	0.393	2e-31
125901787	1222	pol-like protein [Biomphalaria glabrata]	0.570	0.229	0.347	7e-31
443710566	377	hypothetical protein CAPTEDRAFT_186063 [	0.592	0.771	0.296	3e-29
443712830	397	hypothetical protein CAPTEDRAFT_202466 [	0.456	0.564	0.402	7e-28
443713753	266	hypothetical protein CAPTEDRAFT_215116 [	0.450	0.830	0.347	8e-27
443700898	300	hypothetical protein CAPTEDRAFT_212630,	0.553	0.906	0.298	2e-26
443724607	397	hypothetical protein CAPTEDRAFT_208903 [	0.456	0.564	0.389	3e-25
443721618	471	hypothetical protein CAPTEDRAFT_200496,	0.407	0.424	0.341	4e-25
427791321	1210	Putative tick transposon, partial [Rhipi	0.619	0.251	0.321	1e-24

>gi|443693558|gb|ELT94903.1| hypothetical protein CAPTEDRAFT_189741, partial [Capitella teleta]

 Score =  159 bits (401), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 114/295 (38%), Positives = 159/295 (53%), Gaps = 14/295 (4%)

Query: 73  FTTNKP---KPLLSRFQSLPSFPNLISSSDMAPY-VRTVPPWSSPSPPVDLSLGKDRKND 128
           F T+KP   +PLL R +   +  ++I++  +AP+ +  VPPW    P VD S+ K  K+ 
Sbjct: 6   FYTSKPSFIRPLLYRTEE--ALESVITAP-IAPFKISDVPPWKLRPPEVDTSISKFLKDQ 62

Query: 129 TPSVAFQQLFAGVINSKYANYTICYTDGSKTMNTTSCAFSIDDLISSSQLNPVNSIFSAE 188
            P++  +Q F  +I+ KY    I YTDGSK+ N  +CAF+         L    SI++AE
Sbjct: 63  HPALFLKQEFYNLID-KYPGINI-YTDGSKSNNAVACAFTCSTYQIQFGLPTQMSIYTAE 120

Query: 189 LIAIYLCLEAI-TVHPSDQFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVV 247
           LIAI   L  I TV   DQF I SDS S+L ALSN   T+P +  + +  + L  + K+V
Sbjct: 121 LIAIEQALIFIETVKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLV 180

Query: 248 HFLWCPSHCGIRGNEAVDEAARNPVNPTQLKLCSPE-DFKPIAASIVKKEWQNQWDNVPN 306
            F+WCPSH GI GNE  D  A+  +     KL  P  D+K    S VK  WQN+WD   +
Sbjct: 181 VFIWCPSHVGILGNEVADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDEETD 240

Query: 307 TNKLKAIKPLIAPWNTSNQENRTQEIQIKQCEIPASTSLTGYANIYNIPP--IPC 359
            NKL +I+P+I+ W    Q +R  EI + +  I  S    GY     + P  IPC
Sbjct: 241 -NKLHSIQPVISEWKQGPQIDRRGEIVLARARIGHSHLTHGYLLRREVAPFCIPC 294

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443695973|gb|ELT96755.1| hypothetical protein CAPTEDRAFT_23017, partial [Capitella teleta]

 Score =  143 bits (361), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 98/249 (39%), Positives = 132/249 (53%), Gaps = 7/249 (2%)

Query: 115 PPVDLSLGKDRKNDTPSVAFQQLFAGVINSKYANYTICYTDGSKTMNTTSCAFSIDDLIS 174
           P VD S+ K  K+  P++  +Q F  +I+ KY    I YTDGSK+ +  +CAF+      
Sbjct: 3   PEVDTSISKFLKDQHPALFLKQEFYNLID-KYPGINI-YTDGSKSNDAVACAFTCSTYQI 60

Query: 175 SSQLNPVNSIFSAELIAIYLCLEAI-TVHPSDQFLIVSDSRSALAALSNVSFTNPLVSKV 233
              L    SI++AELIAI   L  I TV   DQF I SDS S+L ALSN   T+P +  +
Sbjct: 61  QFGLPAQMSIYTAELIAIEQALIFIETVKDEDQFNICSDSLSSLTALSNCDITHPYLLSI 120

Query: 234 YSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQLKLCSPE-DFKPIAASI 292
            +  + L  + K+V F+WCPSH GI GNE  D  A+  +     KL  P  D+K    S 
Sbjct: 121 LTKQNNLVRKGKLVVFIWCPSHVGILGNEVADRLAKQALVMPVTKLPLPHTDYKSPIRSY 180

Query: 293 VKKEWQNQWDNVPNTNKLKAIKPLIAPWNTSNQENRTQEIQIKQCEIPASTSLTGYANIY 352
           VK  WQN+WD     NKL +I+P+I+ W    Q +R  EI + +  I  S    GY    
Sbjct: 181 VKSLWQNEWDE-ETDNKLHSIQPVISEWKQGPQIDRRGEIVLARARIGHSHLTHGYLLRR 239

Query: 353 NIPP--IPC 359
            + P  IPC
Sbjct: 240 EVAPFCIPC 248

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|125901787|gb|ABN58714.1| pol-like protein [Biomphalaria glabrata]

 Score =  141 bits (356), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 100/288 (34%), Positives = 141/288 (48%), Gaps = 8/288 (2%)

Query: 30   EKEEVHLSLRRSKLLMNYVAKVRASPFNPVQKVLFS-QNLTPYNFTTNKPKPLLSRFQSL 88
            E  E+ + +R  KL M Y+ K++++P NP    +F+   +  YN   N  +PL  R +  
Sbjct: 837  EAGELPMDIRMKKLAMQYIVKLKSNPTNPAFDSIFNPTEVELYNRRPNVIQPLGLRMRE- 895

Query: 89   PSFPNLISSSDMAPYVRT--VPPWSSPSPPVDLSLGKDRKNDTPSVAFQQLFAGVINSKY 146
                NL    D    + T   PPW    P ++LSL   +K +T     Q  F  +  S Y
Sbjct: 896  -PIQNLTQPIDQISKIETPQNPPWLMNKPKLNLSLLNFKKENTDPSILQVHFRELQES-Y 953

Query: 147  ANYTICYTDGSKTMNTTSCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQ 206
             +    YTDGSK     +CA S  +   S +L    SIF+AEL AI L L A+      +
Sbjct: 954  GDCGTIYTDGSKMEGKVACACSFRNKTISRRLPDGCSIFTAELHAILLALMAVKASERSK 1013

Query: 207  FLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDE 266
            F+I SDS+SAL AL  +    PLV K     DL+ +  + V F+W PSH GI GNEA D 
Sbjct: 1014 FIICSDSKSALQALGRMKTDIPLVHKSLKLLDLITADRRDVTFIWVPSHVGIEGNEAADR 1073

Query: 267  AARNPVNPTQLKLCSP-EDFKPIAASIVKKEWQNQWDNVPNTNKLKAI 313
             A+  +N        P  D +   AS   +EWQN+W+     +KL+ I
Sbjct: 1074 EAKRALNHAVSGTQIPYSDLRQSIASATYREWQNRWE-AETHSKLRQI 1120

Source: Biomphalaria glabrata

Species: Biomphalaria glabrata

Genus: Biomphalaria

Family: Planorbidae

Class: Gastropoda

Phylum: Mollusca

Superkingdom: Eukaryota

>gi|443710566|gb|ELU04776.1| hypothetical protein CAPTEDRAFT_186063 [Capitella teleta]

 Score =  135 bits (341), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 93/314 (29%), Positives = 155/314 (49%), Gaps = 23/314 (7%)

Query: 30  EKEEVHLSLRRSKLLMNYVAKVRASPFNPVQKVLFSQNLTPYNFTT-NKPKPLLSRFQSL 88
           E  E+ +++R+  L + +  +V +   NP  + +F+ N   +  +  N  +PL  R +  
Sbjct: 66  EANEMPMAIRQKLLSVQFALRVCSDTTNPAHQCIFNYNNDRFYLSKPNAIRPLALRIKE- 124

Query: 89  PSFPNLISSSDMAPYVRTVPP--------WSSPSPPVDLSLGK-DRKNDTPSVAFQQLFA 139
                      + P ++ + P        W    P +D+SL    +K   P+   +  F 
Sbjct: 125 -------DLQTICPDIKAITPNQLFNIPYWLLRPPELDISLIHFGKKTANPNYTLKNEFY 177

Query: 140 GVINSKYANYTICYTDGSKTMNTTSCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLEAI 199
            +++ KY ++ + +TDGSK+ +  +C  + D+L    +L    SIFSAEL+AIY  L  +
Sbjct: 178 NLMD-KYPDHKVIFTDGSKSDSAVACFATADNLSIQIRLPDSASIFSAELLAIYQVLTLL 236

Query: 200 TVHPSDQ--FLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCG 257
               +DQ  FLI +DS S+L A+ N +  +P V K+     LL  +   +   WCPSH G
Sbjct: 237 ECSANDQQQFLIATDSLSSLQAIGNFNIKHPYVFKILEKCTLLHKKGIYLVMAWCPSHVG 296

Query: 258 IRGNEAVDEAARNPVNPTQLKLCSP-EDFKPIAASIVKKEWQNQWDNVPNTNKLKAIKPL 316
           + GNE  D  A+  ++ T   +  P  DFKPI     K++WQ QW +    NKL  I+P 
Sbjct: 297 VMGNERADLLAKEALSFTTCTIRIPSSDFKPITHEFFKEKWQEQWSS-EQENKLYCIQPT 355

Query: 317 IAPWNTSNQENRTQ 330
           +  W  S++E R +
Sbjct: 356 LGKWAKSSREIRRK 369

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443712830|gb|ELU05953.1| hypothetical protein CAPTEDRAFT_202466 [Capitella teleta]

 Score =  131 bits (330), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 93/231 (40%), Positives = 120/231 (51%), Gaps = 7/231 (3%)

Query: 133 AFQQLFAGVINSKYANYTICYTDGSKTMNTTSCAFSIDDLISSSQLNPVNSIFSAELIAI 192
           AF   F  +I+ KY    I YTDGSK+ +T +CAF+         L    SI++AELIAI
Sbjct: 116 AFNHEFYNLID-KYPGINI-YTDGSKSNDTVACAFTCSTYQIQFGLPAQMSIYTAELIAI 173

Query: 193 YLCLEAI-TVHPSDQFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLW 251
              L  I TV   DQF I SDS S+L ALSN   T+P +  + +  + L  + K V F+W
Sbjct: 174 EQALIFIETVKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKKVVFIW 233

Query: 252 CPSHCGIRGNEAVDEAARNPVNPTQLKLCSPE-DFKPIAASIVKKEWQNQWDNVPNTNKL 310
           CPSH GI GNE  D  A+  +     KL  P  D+K    S VK  WQN+WD   + NKL
Sbjct: 234 CPSHVGILGNEVADRQAKQALVMPVTKLPLPHTDYKSPIRSYVKSLWQNEWDGETD-NKL 292

Query: 311 KAIKPLIAPWNTSNQENRTQEIQIKQCEIPASTSLTGYANIYNIPP--IPC 359
             I+P+I+ W    Q +R  EI +    I  S    GY     + P  IPC
Sbjct: 293 HIIQPVISEWKQGPQIDRRGEIVLACARIGHSHLTHGYLLRREVAPFCIPC 343

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443713753|gb|ELU06453.1| hypothetical protein CAPTEDRAFT_215116 [Capitella teleta]

 Score =  128 bits (321), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 80/230 (34%), Positives = 122/230 (53%), Gaps = 9/230 (3%)

Query: 108 PPWSSPSPPVDLSLGKDRKNDTPSVAFQQLFAGVINSKYANYTICYTDGSKTMNTTSCAF 167
           PPW    P VDLSL   +K+   ++  +  F   ++S Y   T+ YTDGSK+ ++ + +F
Sbjct: 35  PPWHLVQPEVDLSLTFSKKDSMSALTIRSEFEDALDS-YPVSTVFYTDGSKSEDSVARSF 93

Query: 168 SIDDLISSSQLNPVNSIFSAELIAIY---LCLEAITVHPSDQFLIVSDSRSALAALSNVS 224
               L    +L    S+F++E+IAI     CLEA       QF+I SDS SA+ A+  + 
Sbjct: 94  FSSRLKLKMKLPVQMSVFTSEIIAILSALKCLEADN--EQHQFVICSDSLSAIMAIHGMD 151

Query: 225 FTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQL-KLCSP- 282
             +P V +V      +  + K+V F+WCPSH GI GNE     A   ++ T L +L  P 
Sbjct: 152 VHHPYVLQVLYAIKSISQQEKIVVFMWCPSHVGIPGNEMAHTLAEKALSSTNLAELPVPA 211

Query: 283 EDFKPIAASIVKKEWQNQWDNVPNTNKLKAIKPLIAPWNTSNQENRTQEI 332
            D + +    ++ +WQ++W+   N NKL +I P I PW    +E R +EI
Sbjct: 212 SDLRGLIKKYIRSQWQHEWEEQHN-NKLHSIHPTIGPWPPCQREKRREEI 260

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443700898|gb|ELT99633.1| hypothetical protein CAPTEDRAFT_212630, partial [Capitella teleta]

 Score =  127 bits (318), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 88/295 (29%), Positives = 146/295 (49%), Gaps = 23/295 (7%)

Query: 36  LSLRRSKLLMNYVAKVRASPFNPVQKVLFSQNLTPYNFTT-NKPKPLLSRFQSLPSFPNL 94
           +++R+  L + +  +V +   NP  + +F+ N   +  +  N  +PL  R +        
Sbjct: 3   MTIRQKLLSVQFALRVCSDTTNPAHQCIFNYNNDRFYLSKPNAIRPLALRIKE------- 55

Query: 95  ISSSDMAPYVRTVPP--------WSSPSPPVDLSLGK-DRKNDTPSVAFQQLFAGVINSK 145
                + P ++ + P        W    P +D+SL    +K   P+   +  F  +++ K
Sbjct: 56  -DLQTICPDIKAITPNQLFNIPYWLLRPPELDISLIHFGKKTANPNYTLRNEFYNLMD-K 113

Query: 146 YANYTICYTDGSKTMNTTSCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSD 205
           Y ++ + +TDGSK+ +  +C+ + D+L    +L    SIFSAEL+AIY  L  +    +D
Sbjct: 114 YPDHKVIFTDGSKSDSAVACSATADNLRIQIRLPDSASIFSAELLAIYQVLTLLECSAND 173

Query: 206 Q--FLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEA 263
           Q  FLI +DS S+L A+ N +  +P V K+     LL  +   +   WCPSH G+ GNE 
Sbjct: 174 QQQFLIATDSLSSLQAIGNFNIKHPYVFKILQKCTLLHKKGIYLVMAWCPSHVGVMGNER 233

Query: 264 VDEAARNPVNPTQLKLCSP-EDFKPIAASIVKKEWQNQWDNVPNTNKLKAIKPLI 317
            D  A+  ++ T   +  P  DFKPI     K++WQ QW +    NKL  I+P I
Sbjct: 234 ADLLAKEALSFTTCTIRVPSSDFKPITHEFYKEKWQEQWSS-EQENKLYCIQPTI 287

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443724607|gb|ELU12531.1| hypothetical protein CAPTEDRAFT_208903 [Capitella teleta]

 Score =  123 bits (308), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 90/231 (38%), Positives = 119/231 (51%), Gaps = 7/231 (3%)

Query: 133 AFQQLFAGVINSKYANYTICYTDGSKTMNTTSCAFSIDDLISSSQLNPVNSIFSAELIAI 192
           AF   F  +I+ KY    I YTDGSK+ +  +CAF+         L    SI++AELIAI
Sbjct: 116 AFNHEFYNLID-KYPGINI-YTDGSKSNDAVACAFTCSTYQIQFGLPAQMSIYTAELIAI 173

Query: 193 YLCLEAI-TVHPSDQFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLW 251
              L  I T+   DQF I SDS S+L ALSN   T+P +  + +  + L  + K+V F+W
Sbjct: 174 EQALIFIETMKDEDQFNICSDSLSSLTALSNCDITHPYLLSILTKQNNLVRKGKLVVFIW 233

Query: 252 CPSHCGIRGNEAVDEAARNPVNPTQLKLCSPE-DFKPIAASIVKKEWQNQWDNVPNTNKL 310
           CPSH GI GNE  D  A+  +     KL  P  D+K    S VK   QN+WD   + NKL
Sbjct: 234 CPSHVGILGNEVADRLAKQALVMPVTKLPLPHTDYKSPIRSYVKSLRQNEWDEETD-NKL 292

Query: 311 KAIKPLIAPWNTSNQENRTQEIQIKQCEIPASTSLTGYANIYNIPP--IPC 359
             I+P+I+ W    Q +R  EI +    I  S    GY     + P  IPC
Sbjct: 293 HTIQPVISEWKQGPQIDRRGEIVLACACIGHSHLTHGYLLRREVAPFCIPC 343

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|443721618|gb|ELU10867.1| hypothetical protein CAPTEDRAFT_200496, partial [Capitella teleta]

 Score =  122 bits (306), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 70/205 (34%), Positives = 114/205 (55%), Gaps = 5/205 (2%)

Query: 138 FAGVINSKYANYTICYTDGSKTMNTTSCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLE 197
           FA  ++ +Y + T+ YTDGSK+ ++ +C+F    L    +L    S+F++E+IAI   L 
Sbjct: 10  FADALD-RYPDSTVFYTDGSKSEDSVACSFFSSRLKLKMKLPVQMSVFTSEIIAILSALR 68

Query: 198 AITV-HPSDQFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHC 256
            +   +   QF+I SDS SA+ A+  +   +P V +V      +  + K+V F+WCPSH 
Sbjct: 69  CVEADNEQHQFVICSDSLSAIMAIHGMDVRHPYVLQVLYAIKSISQQEKIVVFMWCPSHV 128

Query: 257 GIRGNEAVDEAARNPVNPTQL-KLCSP-EDFKPIAASIVKKEWQNQWDNVPNTNKLKAIK 314
           GI GNE  D  A+  ++ T L +L  P  D + +    ++  WQ++WD   ++NKL +I 
Sbjct: 129 GIPGNEMADTLAKEALSSTNLAELPVPASDLRCLIKKYIRSRWQHEWDE-QHSNKLHSIH 187

Query: 315 PLIAPWNTSNQENRTQEIQIKQCEI 339
           P I PW    +E R +EI + +  I
Sbjct: 188 PTIGPWPPCQREKRREEIVLARIRI 212

Source: Capitella teleta

Species: Capitella teleta

Genus: Capitella

Family: Capitellidae

Order: Capitellida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|427791321|gb|JAA61112.1| Putative tick transposon, partial [Rhipicephalus pulchellus]

 Score =  121 bits (303), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 102/317 (32%), Positives = 150/317 (47%), Gaps = 13/317 (4%)

Query: 36   LSLRRSKLLMNYVAKVRASPFNPVQKVL--FSQNLTPYNFTTNKPKPLLSRFQSLPSFPN 93
            LS RR+ L ++YV ++R+SP +    +    S  L   N  +N  KPLL RF+       
Sbjct: 822  LSHRRASLTLSYVLRIRSSPQHICYDIATRCSSRLHYLN-KSNLIKPLLLRFEEYCR-TY 879

Query: 94   LISSS--DMAPYVRTVPPWSSPSPPVDLSLGKDRKNDTPSVAFQQLFAGVINSKYANYTI 151
            +IS    D+A     +PPW   +   D+SL    K  TP     Q F   +  KY +Y  
Sbjct: 880  VISEETLDVARKPPRIPPWFDLAQLCDISLSHINKKVTPPELIIQEFRA-LQEKYRDYAE 938

Query: 152  CYTDGSKTMNTTSCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVS 211
             YTDGSKT +         +   S ++    SIF+AE+ A+Y     I      + +I +
Sbjct: 939  FYTDGSKTRDHVGIGIVTGESAFSVRVPQCISIFTAEVYALYEAARKIIAGKHKKAIIYT 998

Query: 212  DSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNP 271
            DS SAL AL   S   PLV  + +   L+ S+   + F W PSH GI GNE  D+ A   
Sbjct: 999  DSLSALKALHIKSECEPLVGDILNM-VLINSKVISMRFCWVPSHVGIPGNEKADKCASLA 1057

Query: 272  VNPTQLKLCSP--EDFKPIAASIVKKEWQNQWDNVPNTNKLKAIKPLIAPWNTSNQENRT 329
             + T  K+  P  +  + I  +++ K WQ QWD+   +NKL  +KP +  W     + R 
Sbjct: 1058 AHKTLTKIRIPLKDSQRTIRLALLAK-WQQQWDSC-TSNKLHLVKPTLGEWKNCRHQERF 1115

Query: 330  QEIQIKQCEIPASTSLT 346
             E+ + +  I   T LT
Sbjct: 1116 IEVILCRLRI-GHTHLT 1131

Source: Rhipicephalus pulchellus

Species: Rhipicephalus pulchellus

Genus: Rhipicephalus

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	491
ASPGD|ASPL0000075333	486	AN10625 [Emericella nidulans (	0.331	0.335	0.252	2.1e-05

ASPGD|ASPL0000075333 AN10625 [Emericella nidulans (taxid:162425)]

 Score = 132 (51.5 bits), Expect = 2.1e-05, P = 2.1e-05
 Identities = 44/174 (25%), Positives = 71/174 (40%)

Query:   153 YTDGSKTMNTTSCAFSIDD-LISSSQL---NPVNSIFSAELIAIYLCLEAITVHPSDQFL 208
             YTDGS        A      LIS S        ++++ AEL  I L L  I        +
Sbjct:   186 YTDGSGINGRVGAAAICPKYLISRSSYMGQQSESTVYVAELQGILLALVIILQRQMQHAV 245

Query:   209 IVSDSRSALAALSNVSFTNP--LVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDE 266
             I +D+++ L AL N    +   ++  +    +  R     VHF W P+H G+ GNE  D 
Sbjct:   246 IFTDNQATLQALRNPGSQSGQYILEAIIMALNKGRKAGLNVHFRWIPAHRGVEGNEQADR 305

Query:   267 AARNPVNPTQLK-----LCSPEDFKPIAASIVKKEWQNQWDNVPNTNKLKAIKP 315
              A+      +++     +      K  A  +V   W+N W +  +  +L  + P
Sbjct:   306 RAKEATGWRRIRGHRGRMTIRSAVKRRAHEVVNARWENDWKSCHHGRELYELTP 359


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.318   0.134   0.395    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      491       482   0.00080  119 3  11 22  0.39    34
                                                     35  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  618 (66 KB)
  Total size of DFA:  286 KB (2149 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:04
  No. of threads or processors used:  24
  Search cpu time:  41.50u 0.08s 41.58t   Elapsed:  00:00:15
  Total cpu time:  41.50u 0.08s 41.58t   Elapsed:  00:00:19
  Start:  Thu Aug 15 10:58:11 2013   End:  Thu Aug 15 10:58:30 2013

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004523 "ribonuclease H activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.1.26.4	LOW CONFIDENCE prediction!
3rd Layer	3.1.26	0.691

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	491
cd09276	128	cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI dom	2e-31
pfam00075	126	pfam00075, RNase_H, RNase H	1e-15
cd06222	123	cd06222, RNase_H, RNase H is an endonuclease that	4e-10
cd09273	135	cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase	2e-08
COG0328	154	COG0328, RnhA, Ribonuclease HI [DNA replication, r	4e-04

>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse transcriptases

 Score =  116 bits (294), Expect = 2e-31
 Identities = 45/124 (36%), Positives = 62/124 (50%), Gaps = 5/124 (4%)

Query: 151 ICYTDGSKTMNTTSCAFSI--DDLIS-SSQLNPVNSIFSAELIAIYLCLEAITV--HPSD 205
           + YTDGSK    T   F+I     IS S +L P  S+F AEL+AI   L+        + 
Sbjct: 1   VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60

Query: 206 QFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVD 265
           +  I SDS++AL AL +   ++PLV ++      L +    V   W P H GI GNE  D
Sbjct: 61  KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERAD 120

Query: 266 EAAR 269
             A+
Sbjct: 121 RLAK 124

Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 128

>gnl|CDD|215695 pfam00075, RNase_H, RNase H

 Score = 73.1 bits (180), Expect = 1e-15
 Identities = 35/128 (27%), Positives = 55/128 (42%), Gaps = 13/128 (10%)

Query: 148 NYTICYTDGS--KTMNTTSCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSD 205
                YTDGS           +  D     S+  P  +   AEL+A+   LEA+      
Sbjct: 2   EAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALEAL---SGQ 58

Query: 206 QFLIVSDSR----SALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGN 261
           +  I +DS+             S + P+ ++    W+LL+ ++KV +  W P H GI GN
Sbjct: 59  KVNIYTDSQYVIGGITNGWPTKSESKPIKNE---IWELLQKKHKV-YIQWVPGHSGIPGN 114

Query: 262 EAVDEAAR 269
           E  D+ A+
Sbjct: 115 ELADKLAK 122

RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers. Length = 126

>gnl|CDD|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner

 Score = 57.4 bits (139), Expect = 4e-10
 Identities = 28/126 (22%), Positives = 45/126 (35%), Gaps = 11/126 (8%)

Query: 153 YTDGSKTMNTTSCAF-------SIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSD 205
            TDGS   N                 L + S   P  +   AEL+A+   LE        
Sbjct: 1   NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60

Query: 206 QFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVD 265
           + +I +DS+  +  +++ S      + +     LL S+   + F   P      GNE  D
Sbjct: 61  KLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEVAD 116

Query: 266 EAARNP 271
             A+  
Sbjct: 117 RLAKEA 122

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 123

>gnl|CDD|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term repeat retroelements

 Score = 52.3 bits (126), Expect = 2e-08
 Identities = 33/134 (24%), Positives = 49/134 (36%), Gaps = 19/134 (14%)

Query: 152 CYTDGSKTMNTTSCA-FSIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIV 210
            +TDGS  +     A  +  D++  + L    S   AELIA+   + A+ +       I 
Sbjct: 2   VFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIAL---IRALELAKGKPVNIY 58

Query: 211 SDSRSALAALS-------NVSFTNPLVSKVYSCWDLLR---SRNKVVHFLWCPSHCG--- 257
           +DS  A   L           F       + S    L+    R K V  +   +H G   
Sbjct: 59  TDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKPVAVIHIRAHSGLPG 118

Query: 258 --IRGNEAVDEAAR 269
               GN   D+AAR
Sbjct: 119 PLALGNARADQAAR 132

Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamatic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. Length = 135

>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and repair]

 Score = 40.4 bits (95), Expect = 4e-04
 Identities = 23/95 (24%), Positives = 38/95 (40%), Gaps = 12/95 (12%)

Query: 187 AELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNVSFTNPLVS---------KVYSCW 237
           AEL A+   LEA+    + +  + +DS+  +  ++                   K    W
Sbjct: 46  AELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLW 105

Query: 238 ---DLLRSRNKVVHFLWCPSHCGIRGNEAVDEAAR 269
              D L  R+++V + W   H G   NE  D+ AR
Sbjct: 106 EELDELLKRHELVFWEWVKGHAGHPENERADQLAR 140

Length = 154

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	491
PRK06548	161	ribonuclease H; Provisional	99.82
PRK08719	147	ribonuclease H; Reviewed	99.81
COG0328	154	RnhA Ribonuclease HI [DNA replication, recombinati	99.8
PF00075	132	RNase_H: RNase H; InterPro: IPR002156 The RNase H	99.79
PRK00203	150	rnhA ribonuclease H; Reviewed	99.79
cd06222	130	RnaseH RNase H (RNase HI) is an endonuclease that	99.69
KOG3752|consensus	371		99.59
PRK13907	128	rnhA ribonuclease H; Provisional	99.55
PRK07708	219	hypothetical protein; Validated	99.41
PRK07238	372	bifunctional RNase H/acid phosphatase; Provisional	99.24
PF13456	87	RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EH	98.99
PF13966	86	zf-RVT: zinc-binding in reverse transcriptase	91.24

>PRK06548 ribonuclease H; Provisional

Probab=99.82  E-value=4.3e-20  Score=170.32  Aligned_cols=128  Identities=26%  Similarity=0.255  Sum_probs=93.6

Q ss_pred             CCceEEEecCCCCC--CCceeEeeeCCeeeEeecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHhc--
Q psy9180         147 ANYTICYTDGSKTM--NTTSCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSN--  222 (491)
Q Consensus       147 ~~~i~IyTDGS~~~--~~vG~g~v~~~~~~~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~~--  222 (491)
                      +..+.||||||+..  +..|+|++.............+|++.|||.|++.||+.+.. ....+.|+|||++|++++..  
T Consensus         3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~   81 (161)
T PRK06548          3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWV   81 (161)
T ss_pred             CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHH
Confidence            34599999999884  45778876543222222234689999999999999987653 34579999999999999994  


Q ss_pred             -------ccCCC--CCcchhHHHHH-HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCCCCC
Q psy9180         223 -------VSFTN--PLVSKVYSCWD-LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQ  276 (491)
Q Consensus       223 -------~~~~~--~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~~~  276 (491)
                             ++..+  |...+++.++| .+... ..|+|.|||||+|++|||.||+||++|+....
T Consensus        82 ~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~~  144 (161)
T PRK06548         82 YSWKMRKWRKADGKPVLNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANNFS  144 (161)
T ss_pred             HHHHHCCCcccCCCccccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHHhc
Confidence                   22221  22235566777 33333 47999999999999999999999999886543

>PRK08719 ribonuclease H; Reviewed

Probab=99.81  E-value=1.3e-19  Score=165.39  Aligned_cols=121  Identities=24%  Similarity=0.228  Sum_probs=88.8

Q ss_pred             CceEEEecCCCCCCC-----ceeEeee--CC--e--eeEeecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHH
Q psy9180         148 NYTICYTDGSKTMNT-----TSCAFSI--DD--L--ISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSA  216 (491)
Q Consensus       148 ~~i~IyTDGS~~~~~-----vG~g~v~--~~--~--~~~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsa  216 (491)
                      ..++||||||+.+++     .|+|++.  .+  .  ..+..+....|++.||+.|+..||+.+.+.    ..|+|||++|
T Consensus         3 ~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yv   78 (147)
T PRK08719          3 ASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYC   78 (147)
T ss_pred             ceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHH
Confidence            568999999997432     4788653  22  1  233345556899999999999999998753    3799999999


Q ss_pred             HHHHh--------cccCCC---CCcchhHHHHH-HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCC
Q psy9180         217 LAALS--------NVSFTN---PLVSKVYSCWD-LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVN  273 (491)
Q Consensus       217 l~aL~--------~~~~~~---~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~  273 (491)
                      ++++.        +.+..+   |....++.+.| .+.. ...|+|.|||||+|++|||.||+||++|++
T Consensus        79 i~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~  146 (147)
T PRK08719         79 VRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE  146 (147)
T ss_pred             HHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence            99984        332211   11123445566 3444 567999999999999999999999999875

>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]

Probab=99.80  E-value=1.9e-19  Score=163.68  Aligned_cols=128  Identities=20%  Similarity=0.158  Sum_probs=97.6

Q ss_pred             CceEEEecCCCCC--CCceeEeee--CCeeeEeec-CCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHhc
Q psy9180         148 NYTICYTDGSKTM--NTTSCAFSI--DDLISSSQL-NPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSN  222 (491)
Q Consensus       148 ~~i~IyTDGS~~~--~~vG~g~v~--~~~~~~~~l-~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~~  222 (491)
                      ..+.||||||+..  |..|+|+|.  ++....++. -..+|++.||+.|++.||+.+.+.+...|.|+|||++++++|..
T Consensus         2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~   81 (154)
T COG0328           2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITR   81 (154)
T ss_pred             CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeeecccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHH
Confidence            3578999999983  446777663  332222222 23899999999999999999998888999999999999999995


Q ss_pred             ccCCCC-----------CcchhHHHHH-HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCCCC
Q psy9180         223 VSFTNP-----------LVSKVYSCWD-LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPT  275 (491)
Q Consensus       223 ~~~~~~-----------~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~~  275 (491)
                      +...++           ....++.+++ .+..+...|.+.|||||+|.++||.||+||+.|++..
T Consensus        82 w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~  146 (154)
T COG0328          82 WIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA  146 (154)
T ss_pred             HHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence            423221           1123345555 5556666999999999999999999999999998765

>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site

Probab=99.79  E-value=1.1e-19  Score=161.12  Aligned_cols=121  Identities=30%  Similarity=0.294  Sum_probs=87.4

Q ss_pred             CceEEEecCCCCC--CCceeEee-eCCeeeEeecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHhccc
Q psy9180         148 NYTICYTDGSKTM--NTTSCAFS-IDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNVS  224 (491)
Q Consensus       148 ~~i~IyTDGS~~~--~~vG~g~v-~~~~~~~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~~~~  224 (491)
                      +.+.||||||..+  +..|+|++ ..+......++ ..+++.|||.||..||+.+ .  .+.+.|+|||+++++.+..+.
T Consensus         2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~v~~~l~~~~   77 (132)
T PF00075_consen    2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL-E--HRKVTIYTDSQYVLNALNKWL   77 (132)
T ss_dssp             TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH-S--TSEEEEEES-HHHHHHHHTHH
T ss_pred             CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh-h--cccccccccHHHHHHHHHHhc
Confidence            5689999999763  33466654 33333344455 8999999999999999954 3  389999999999999887721


Q ss_pred             C--CCCCc-ch-hHHHHH-HhhcCCCeEEEEEeeccCCC-CCChHHhHHhhCCC
Q psy9180         225 F--TNPLV-SK-VYSCWD-LLRSRNKVVHFLWCPSHCGI-RGNEAVDEAARNPV  272 (491)
Q Consensus       225 ~--~~~~~-~~-~~~~~I-~l~~~~~~V~~~WVPgH~gi-~gNE~AD~lAk~A~  272 (491)
                      .  .++.. .. .+..+| .+...+..|.|+|||||+|+ .|||.||+|||+|+
T Consensus        78 ~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~  131 (132)
T PF00075_consen   78 HGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAA  131 (132)
T ss_dssp             HHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence            1  11111 11 244455 33355889999999999999 69999999999875

This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....

>PRK00203 rnhA ribonuclease H; Reviewed

Probab=99.79  E-value=5.2e-19  Score=161.92  Aligned_cols=125  Identities=18%  Similarity=0.165  Sum_probs=91.0

Q ss_pred             ceEEEecCCCCC--CCceeEeee--CCeeeEe-ecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHhcc
Q psy9180         149 YTICYTDGSKTM--NTTSCAFSI--DDLISSS-QLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNV  223 (491)
Q Consensus       149 ~i~IyTDGS~~~--~~vG~g~v~--~~~~~~~-~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~~~  223 (491)
                      .+.||||||+.+  +..|+|++.  .+....+ ......|++.|||.|+..||+.+.+  ...+.|+|||++++++|..+
T Consensus         3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w   80 (150)
T PRK00203          3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEW   80 (150)
T ss_pred             eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHH
Confidence            488999999983  346777653  3322222 2235678999999999999998865  46899999999999999863


Q ss_pred             cC---------C--CCCcchhHHHHH-HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCCCCC
Q psy9180         224 SF---------T--NPLVSKVYSCWD-LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQ  276 (491)
Q Consensus       224 ~~---------~--~~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~~~  276 (491)
                      ..         .  .|....++.++| .+. ....|.|.|||||+|++||+.||+|||+|+....
T Consensus        81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~-~~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~  144 (150)
T PRK00203         81 IHGWKKNGWKTADKKPVKNVDLWQRLDAAL-KRHQIKWHWVKGHAGHPENERCDELARAGAEEAT  144 (150)
T ss_pred             HHHHHHcCCcccCCCccccHHHHHHHHHHh-ccCceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence            11         1  111223455666 332 3478999999999999999999999999886543

>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner

Probab=99.69  E-value=2.3e-16  Score=135.65  Aligned_cols=122  Identities=28%  Similarity=0.296  Sum_probs=93.3

Q ss_pred             EEEecCCCCCC--CceeEeeeCC--eeeE---eecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHhcc
Q psy9180         151 ICYTDGSKTMN--TTSCAFSIDD--LISS---SQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNV  223 (491)
Q Consensus       151 ~IyTDGS~~~~--~vG~g~v~~~--~~~~---~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~~~  223 (491)
                      .+|||||...+  +.|+|++..+  ....   .......+++.||+.|+..||+.+......++.|++||+.++..+.+.
T Consensus         1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~   80 (130)
T cd06222           1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGW   80 (130)
T ss_pred             CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcc
Confidence            48999999854  6788876432  1111   112257899999999999999999888889999999999999999986


Q ss_pred             cCCCCCcchhHHHHH-HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCC
Q psy9180         224 SFTNPLVSKVYSCWD-LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPV  272 (491)
Q Consensus       224 ~~~~~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~  272 (491)
                      ....+.....+...+ .+......+.|.|||+|+|+.+|+.||.+||+|.
T Consensus        81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~  130 (130)
T cd06222          81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA  130 (130)
T ss_pred             ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence            531111223344555 3335678999999999999999999999999874

One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.

>KOG3752|consensus

Probab=99.59  E-value=4.6e-15  Score=150.23  Aligned_cols=127  Identities=24%  Similarity=0.199  Sum_probs=98.5

Q ss_pred             CCceEEEecCCCCC-----CCceeEeeeCC---eeeEeecC-CCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHH
Q psy9180         147 ANYTICYTDGSKTM-----NTTSCAFSIDD---LISSSQLN-PVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSAL  217 (491)
Q Consensus       147 ~~~i~IyTDGS~~~-----~~vG~g~v~~~---~~~~~~l~-~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal  217 (491)
                      .+..++|||||+..     ..+|+|++.++   ...+..+. ..+++|.|||.|+..||+.+.+....+++|.|||+.++
T Consensus       210 ~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i  289 (371)
T KOG3752|consen  210 IEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFI  289 (371)
T ss_pred             ccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHH
Confidence            44589999999884     24899998653   34566664 88999999999999999999987778999999999999


Q ss_pred             HHHhcccCCCC---C---cchh----------HHHHH-Hh-hc-CCCeEEEEEeeccCCCCCChHHhHHhhCCCC
Q psy9180         218 AALSNVSFTNP---L---VSKV----------YSCWD-LL-RS-RNKVVHFLWCPSHCGIRGNEAVDEAARNPVN  273 (491)
Q Consensus       218 ~aL~~~~~~~~---~---~~~~----------~~~~I-~l-~~-~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~  273 (491)
                      +.|+.+.+.+.   +   ..++          .+..+ .| +. ++.+|++.|||||.|+.|||.||.+|+++..
T Consensus       290 ~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~  364 (371)
T KOG3752|consen  290 NSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGST  364 (371)
T ss_pred             HHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhh
Confidence            99987655321   1   0111          12222 22 22 5789999999999999999999999999854

>PRK13907 rnhA ribonuclease H; Provisional

Probab=99.55  E-value=1.8e-14  Score=128.09  Aligned_cols=120  Identities=19%  Similarity=0.136  Sum_probs=90.4

Q ss_pred             eEEEecCCCCC--CCceeEeeeCCe--eeEee-cCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHhccc
Q psy9180         150 TICYTDGSKTM--NTTSCAFSIDDL--ISSSQ-LNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNVS  224 (491)
Q Consensus       150 i~IyTDGS~~~--~~vG~g~v~~~~--~~~~~-l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~~~~  224 (491)
                      ++||||||...  +..|+|++..+.  ....+ .....+++.||+.|++.||+.+...+..++.|+|||+.+++.+++..
T Consensus         2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~   81 (128)
T PRK13907          2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEY   81 (128)
T ss_pred             EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHH
Confidence            67999999884  567888774322  11122 23467899999999999999999988889999999999999999855


Q ss_pred             CCCCCcchhHHHHH-HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCCC
Q psy9180         225 FTNPLVSKVYSCWD-LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNP  274 (491)
Q Consensus       225 ~~~~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~  274 (491)
                      .+.+ .-..+.+++ .+......+.|.|||.    +.|+.||.+|++|...
T Consensus        82 ~~~~-~~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~  127 (128)
T PRK13907         82 AKNK-MFAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAILQ  127 (128)
T ss_pred             hcCh-hHHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence            3221 123445555 4455666788899996    5999999999998753

>PRK07708 hypothetical protein; Validated

Probab=99.41  E-value=1.9e-12  Score=125.52  Aligned_cols=129  Identities=13%  Similarity=0.075  Sum_probs=92.3

Q ss_pred             cCCCceEEEecCCCC--CCCceeEeee--CCe--ee----EeecCCCccchHHHHHHHHHHHHHHHcCCCC--eEEEEcc
Q psy9180         145 KYANYTICYTDGSKT--MNTTSCAFSI--DDL--IS----SSQLNPVNSIFSAELIAIYLCLEAITVHPSD--QFLIVSD  212 (491)
Q Consensus       145 ~~~~~i~IyTDGS~~--~~~vG~g~v~--~~~--~~----~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~--~i~I~tD  212 (491)
                      ..++.+++|+|||..  +++.|+|++.  .+.  ..    ...+....|++.||+.|++.||+.+.+.+.+  .|.|++|
T Consensus        69 ~ep~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~D  148 (219)
T PRK07708         69 EEPHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGD  148 (219)
T ss_pred             cCCCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEec
Confidence            356789999999986  3567888663  221  11    1234556899999999999999999987654  4899999


Q ss_pred             cHHHHHHHhcccCCCCCcchhHHHHH--HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCCCCCC
Q psy9180         213 SRSALAALSNVSFTNPLVSKVYSCWD--LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQL  277 (491)
Q Consensus       213 Sqsal~aL~~~~~~~~~~~~~~~~~I--~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~~~~  277 (491)
                      |+.+++.+.+.+.......+.+...+  .+..-...+.+.|||    ...|+.||+||++|++...+
T Consensus       149 SqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~~  211 (219)
T PRK07708        149 SQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTVI  211 (219)
T ss_pred             cHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCCC
Confidence            99999999975421111113344444  333444567889997    57899999999999986654

>PRK07238 bifunctional RNase H/acid phosphatase; Provisional

Probab=99.24  E-value=3.5e-11  Score=125.82  Aligned_cols=123  Identities=17%  Similarity=0.142  Sum_probs=90.2

Q ss_pred             ceEEEecCCCCC--CCceeEeee--CCee---eEe-ecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHH
Q psy9180         149 YTICYTDGSKTM--NTTSCAFSI--DDLI---SSS-QLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAAL  220 (491)
Q Consensus       149 ~i~IyTDGS~~~--~~vG~g~v~--~~~~---~~~-~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL  220 (491)
                      .+.||||||...  +..|+|++.  .+..   ..+ .....+|++.||+.|++.||+.+.+.+.+.+.|++||+.+++.+
T Consensus         2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i   81 (372)
T PRK07238          2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQM   81 (372)
T ss_pred             eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHh
Confidence            368999999984  357888763  2211   112 22236788999999999999999998888999999999999999


Q ss_pred             hcccC-CCCCcchhHHHHH-HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCCCCC
Q psy9180         221 SNVSF-TNPLVSKVYSCWD-LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQ  276 (491)
Q Consensus       221 ~~~~~-~~~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~~~  276 (491)
                      .+.+. +++. -..+..++ .+......+.+.|||.    .+|+.||.||++|.....
T Consensus        82 ~~~~~~~~~~-l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~~~  134 (372)
T PRK07238         82 SGRWKVKHPD-MKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDAAA  134 (372)
T ss_pred             CCCCccCChH-HHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHhhc
Confidence            87542 1110 12234444 4555667899999995    799999999999976544

>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B

Probab=98.99  E-value=1.6e-09  Score=88.57  Aligned_cols=84  Identities=19%  Similarity=0.090  Sum_probs=65.8

Q ss_pred             chHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHhcccCCCCCcchhHHHHH-HhhcCCCeEEEEEeeccCCCCCCh
Q psy9180         184 IFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNVSFTNPLVSKVYSCWD-LLRSRNKVVHFLWCPSHCGIRGNE  262 (491)
Q Consensus       184 v~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~~~~~~~~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE  262 (491)
                      +..||+.|+..||+.+.+.+.+++.|.|||+.++..+++...... ....+++.| .+......+.+.|||    .++|.
T Consensus         1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~-~~~~~~~~i~~~~~~~~~~~~~~i~----r~~N~   75 (87)
T PF13456_consen    1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRS-ELRPLIQDIRSLLDRFWNVSVSHIP----REQNK   75 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---S-CCHHHHHHHHHHHCCCSCEEEEE------GGGSH
T ss_pred             CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccc-cccccchhhhhhhccccceEEEEEC----hHHhH
Confidence            467999999999999999999999999999999999988643222 234566777 566668899999999    68999


Q ss_pred             HHhHHhhCCC
Q psy9180         263 AVDEAARNPV  272 (491)
Q Consensus       263 ~AD~lAk~A~  272 (491)
                      .||.|||.|.
T Consensus        76 ~A~~LA~~a~   85 (87)
T PF13456_consen   76 VADALAKFAL   85 (87)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHh
Confidence            9999999874

>PF13966 zf-RVT: zinc-binding in reverse transcriptase

Probab=91.24  E-value=0.12  Score=42.50  Aligned_cols=27  Identities=19%  Similarity=0.252  Sum_probs=19.5

Q ss_pred             cccCCCCCCC--Ccc--cCcceeeecCCCCh
Q psy9180         349 ANIYNIPPIP--CLI--DHVIHSIHGIPTKS  375 (491)
Q Consensus       349 l~~~~~sp~c--CG~--eTv~H~L~~Cp~~~  375 (491)
                      +.+...++.|  |+.  ||++|++++||.-.
T Consensus        53 ~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~   83 (86)
T PF13966_consen   53 RRGIQVDPICPLCGNEEETIEHLFFHCPFAR   83 (86)
T ss_pred             ccCCccCCccccCCCccccccceeccCcCcc
Confidence            3444455545  874  99999999999754

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	491
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-04
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	3e-08
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	1e-06
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	7e-05
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	6e-04

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 69.1 bits (168), Expect = 2e-12
 Identities = 87/492 (17%), Positives = 155/492 (31%), Gaps = 134/492 (27%)

Query: 7   IIGELEELFY--INCKNNNNIEQLEE----KEEV-HL-----SLRRSKLLMNYVAKVRAS 54
           I+   E+ F    +CK+   ++ + +    KEE+ H+     ++  +  L      + + 
Sbjct: 21  ILSVFEDAFVDNFDCKD---VQDMPKSILSKEEIDHIIMSKDAVSGTLRLFW---TLLSK 74

Query: 55  PFNPVQKVLFSQNLTP-YNFTTNKPKPLLSRFQSLPSFPNLISSSDMAPYVRTVPP-WSS 112
               VQK    + L   Y F       L+S  ++    P    S     Y+      ++ 
Sbjct: 75  QEEMVQK-FVEEVLRINYKF-------LMSPIKTEQRQP----SMMTRMYIEQRDRLYND 122

Query: 113 PSPPVDLSLGKDRKNDTPSVAFQQLFAGVINSKYANYTICYTD-GS-KT----------- 159
                  ++ + +        + +L   ++  + A   +     GS KT           
Sbjct: 123 NQVFAKYNVSRLQP-------YLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYK 175

Query: 160 -----------MNTTSCAFSIDDLIS-----SSQLNPVNSIFSAELIAIYLCLEAITVHP 203
                      +N  +C  S + ++        Q++P  +  S     I L + +I    
Sbjct: 176 VQCKMDFKIFWLNLKNC-NSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAEL 234

Query: 204 SDQFLIVSDSRSALAALSNVSFTNPLVSKVY--SCWDLLRSRNK-VVHFLWCPSHCGIRG 260
               L      + L  L NV   N      +  SC  LL +R K V  FL   +   I  
Sbjct: 235 RR-LLKSKPYENCLLVLLNVQ--NAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISL 291

Query: 261 NEAV-----DEA-------ARNPVN--PTQLKLCSPEDFKPIAASIVKKEWQNQWDNVP- 305
           +        DE                P ++   +P     IA SI  ++    WDN   
Sbjct: 292 DHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESI--RDGLATWDNWKH 349

Query: 306 -NTNKL-KAIKPLIAPWNTSNQENRTQEIQIKQCEIPASTSLTGYANIYNIPPIPCLIDH 363
            N +KL   I+  +     +        + +     P S          +IP        
Sbjct: 350 VNCDKLTTIIESSLNVLEPAEYRKMFDRLSV----FPPSA---------HIPT------I 390

Query: 364 VIHSIHGIPTKSEVIIELFSEVLLSKLHNSGVVESRSYTKV-------LLLTEFVPIMTE 416
           ++  I     KS+V       V+++KLH   +VE +            L L   +     
Sbjct: 391 LLSLIWFDVIKSDV------MVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYA 444

Query: 417 LVPILTDPTHRS 428
           L        HRS
Sbjct: 445 L--------HRS 448

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 42.9 bits (100), Expect = 2e-04
 Identities = 42/371 (11%), Positives = 101/371 (27%), Gaps = 86/371 (23%)

Query: 128 DTPSVAFQQLFAGVINSKYANY-----TICYTDGSKTMNTTSCAFSIDDLISSSQLNPVN 182
                  Q+    V+     NY      I       +M T       D L + +Q+    
Sbjct: 73  SKQEEMVQKFVEEVLR---INYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKY 129

Query: 183 SIFSAELI-AIYLCLEAITVHPSDQFLIV----SDSRSALAA--LSNVSFTNPLVSKVYS 235
           ++   +    +   L  +        +++       ++ +A     +      +  K++ 
Sbjct: 130 NVSRLQPYLKLRQALLELRPAK---NVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIF- 185

Query: 236 CW----------DLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQLKLCSPEDF 285
            W           +L    K+++ +              D ++   +    ++     + 
Sbjct: 186 -WLNLKNCNSPETVLEMLQKLLYQIDPN------WTSRSDHSSNIKLRIHSIQ----AEL 234

Query: 286 KPIAASIVKKEWQNQW---DNVPNTNKLKAIKPLIAPWNTSNQENRTQEIQIKQCEIPAS 342
           + +   +  K ++N      NV N     A                        C+I  +
Sbjct: 235 RRL---LKSKPYENCLLVLLNVQNAKAWNAFNL--------------------SCKILLT 271

Query: 343 T---SLTGYANIYNIPPIPCLIDHVIHSIHGIPTKSEVIIELFSEVLLSKLHNSGVVESR 399
           T    +T + +      I      + H    + T  EV   L  + L  +  +      R
Sbjct: 272 TRFKQVTDFLSAATTTHIS-----LDHHSMTL-TPDEVK-SLLLKYLDCRPQD----LPR 320

Query: 400 SYTKVLLLTEFVPIMTELVPILTDPTHRSYTQVLLLTEFVPIMTEFVPILTDPTHR--YR 457
                      + I+ E +            + +   +   I+   + +L    +R  + 
Sbjct: 321 EVLTTNPRR--LSIIAESIRD--GLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFD 376

Query: 458 YLPILTELVPI 468
            L +      I
Sbjct: 377 RLSVFPPSAHI 387

>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A Length = 165

 Score = 52.2 bits (125), Expect = 3e-08
 Identities = 36/137 (26%), Positives = 52/137 (37%), Gaps = 21/137 (15%)

Query: 147 ANYTICYTDGSKTMNT----TSCAFSIDD-LISSSQLNPVNSIFSAELIAIYLCLEAITV 201
           A+YT  YTDGS  +         A + +  +I +  L    S   AELIA+   L+    
Sbjct: 22  ADYTW-YTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA-- 78

Query: 202 HPSDQFLIVSDSRSALAALSNVSFTNPLVSKVYSCW----DLLRSRNKVVHFLWCPSHCG 257
               +  + +DSR A A     S       K  +        L    ++   + CP H  
Sbjct: 79  -EGKKLNVYTDSRYAFATAHVHSEGRE--IKNKNEILALLKALFLPKRL-SIIHCPGHQK 134

Query: 258 -----IRGNEAVDEAAR 269
                 RGN   D+AAR
Sbjct: 135 GNSAEARGNRMADQAAR 151

>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A Length = 147

 Score = 47.3 bits (113), Expect = 1e-06
 Identities = 21/126 (16%), Positives = 41/126 (32%), Gaps = 12/126 (9%)

Query: 153 YTDGSKTMNTTSCAFSI------DDLISSSQLNPVNSI---FSAELIAIYLCLEAITVHP 203
           YTDGS      + A++           +    NP  +     + E+ A    ++  +   
Sbjct: 10  YTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLG 69

Query: 204 SDQFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEA 263
             +  I+ D        +         ++ Y    L+     +  F    +H G   N+ 
Sbjct: 70  V-KIRILHDYAGIAFWATGEWKAKNEFTQAY--AKLMNQYRGIYSFEKVKAHSGNEFNDY 126

Query: 264 VDEAAR 269
           VD  A+
Sbjct: 127 VDMKAK 132

>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ... Length = 557

 Score = 44.4 bits (105), Expect = 7e-05
 Identities = 28/82 (34%), Positives = 42/82 (51%), Gaps = 10/82 (12%)

Query: 187 AELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSN--VSFTNPLVSKVYSCWDLLRSRN 244
            EL AIYL L+        +  IV+DS+ AL  +        + LV+++    + L  + 
Sbjct: 479 TELQAIYLALQ----DSGLEVNIVTDSQYALGIIQAQPDKSESELVNQII---EQLIKKE 531

Query: 245 KVVHFLWCPSHCGIRGNEAVDE 266
           KV +  W P+H GI GNE VD+
Sbjct: 532 KV-YLAWVPAHKGIGGNEQVDK 552

>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B Length = 555

 Score = 41.3 bits (97), Expect = 6e-04
 Identities = 18/82 (21%), Positives = 38/82 (46%), Gaps = 10/82 (12%)

Query: 187 AELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSN--VSFTNPLVSKVYSCWDLLRSRN 244
           AEL A  + L         +  I+ DS+  +  +++      + +V+++    + +  + 
Sbjct: 476 AELEAFAMALT----DSGPKVNIIVDSQYVMGIVASQPTESESKIVNQII---EEMIKKE 528

Query: 245 KVVHFLWCPSHCGIRGNEAVDE 266
            + +  W P+H GI GN+ VD 
Sbjct: 529 AI-YVAWVPAHKGIGGNQEVDH 549

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	491
2qkb_A	154	Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hy	99.85
3qio_A	150	GAG-POL polyprotein; RNAse H, inhibitor, nuclease,	99.85
3h08_A	146	RNH (ribonuclease H); RNAse H, 3D-structure, endon	99.82
3p1g_A	165	Xenotropic murine leukemia virus-related virus (X	99.81
2kq2_A	147	Ribonuclease H-related protein; PSI, NESG, protein	99.81
1jl1_A	155	Ribonuclease HI; RNAse HI, protein stability, ther	99.8
2e4l_A	158	Ribonuclease HI, RNAse HI; hydrolase, endoribonucl	99.79
1ril_A	166	Ribonuclease H; hydrolase(endoribonuclease); 2.80A	99.78
2lsn_A	165	Reverse transcriptase; RNAse H, viral protein; NMR	99.74
1mu2_A	555	HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polym	99.69
2zd1_A	557	Reverse transcriptase/ribonuclease H; P51/P66, het	99.69
3hst_B	141	Protein RV2228C/MT2287; ribonuclease H1, RV2228C N	99.68
3u3g_D	140	Ribonuclease H, RNAse H1; hydrolase, cleave the RN	99.68
2ehg_A	149	Ribonuclease HI; RNAse HI, hyperthermophilic archa	99.65
1zbf_A	142	Ribonuclease H-related protein; RNAse H, RNA/DNA h	99.08
4htu_A	134	Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine,	98.77

>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A*

Probab=99.85  E-value=1.2e-21  Score=178.49  Aligned_cols=129  Identities=17%  Similarity=0.235  Sum_probs=99.0

Q ss_pred             CCCceEEEecCCCCC-CC----ceeEeeeCCe---eeEeecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHH
Q psy9180         146 YANYTICYTDGSKTM-NT----TSCAFSIDDL---ISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSAL  217 (491)
Q Consensus       146 ~~~~i~IyTDGS~~~-~~----vG~g~v~~~~---~~~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal  217 (491)
                      ..+.+.||||||+.. ++    .|+|++..+.   ..+..+...+|++.||+.|++.||+.+.+.+..++.|+|||++++
T Consensus         4 ~~~~~~iytDGs~~~n~~~~~~aG~Gvv~~~~~~~~~~~~l~~~~tn~~aEl~A~~~aL~~~~~~~~~~v~i~tDS~~vi   83 (154)
T 2qkb_A            4 MGDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKTQNINKLVLYTNSMFTI   83 (154)
T ss_dssp             ETTEEEEEEEEEEETTTSSSCEEEEEEECSTTCTTCEEEECCSSCCHHHHHHHHHHHHHHHHHHTTCCEEEEEESCHHHH
T ss_pred             CCCeEEEEEccCcCCCCCCCCcEEEEEEEECCCceeEEeecCCCCchHHHHHHHHHHHHHHHHhCCCceEEEEECcHHHH
Confidence            357789999999874 32    6888775421   234456557899999999999999999887778999999999999


Q ss_pred             HHHhccc---------CCC--CCcchhHHHHH-HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCCCC
Q psy9180         218 AALSNVS---------FTN--PLVSKVYSCWD-LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPT  275 (491)
Q Consensus       218 ~aL~~~~---------~~~--~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~~  275 (491)
                      +.|.++.         ...  +....++.++| .+. .+..|.|.|||||+|++|||.||+|||+|+...
T Consensus        84 ~~i~~~~~~w~~~~w~~~~~~~~~n~~l~~~i~~l~-~~~~v~~~~V~~H~g~~~N~~AD~LA~~a~~~~  152 (154)
T 2qkb_A           84 NGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLT-QGMDIQWMHVPGHSGFIGNEEADRLAREGAKQS  152 (154)
T ss_dssp             HHHHTHHHHHHTTTSBCTTSSBCTTHHHHHHHHHHH-TTCEEEEEECCTTSSCHHHHHHHHHHHHHHTCC
T ss_pred             hhhhhhHHHHHhccccccCCCccccHHHHHHHHHHH-cCCceEEEEccCCCCCHhHHHHHHHHHHHHHhc
Confidence            9998742         111  11224556666 332 356799999999999999999999999998653

>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase, hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} SCOP: c.55.3.1 PDB: 3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A

Probab=99.85  E-value=2e-21  Score=176.66  Aligned_cols=125  Identities=23%  Similarity=0.288  Sum_probs=93.6

Q ss_pred             cCCCceEEEecCCCCC--CCceeEeeeCC-eeeEeecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHh
Q psy9180         145 KYANYTICYTDGSKTM--NTTSCAFSIDD-LISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALS  221 (491)
Q Consensus       145 ~~~~~i~IyTDGS~~~--~~vG~g~v~~~-~~~~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~  221 (491)
                      ..++.+.||||||+..  +..|+|++... ......+ ..+|++.||+.|+..||+.+    ..++.|+|||++++++|.
T Consensus         8 P~~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~Tnn~aEl~A~i~AL~~~----~~~v~i~tDS~~v~~~i~   82 (150)
T 3qio_A            8 PIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIT   82 (150)
T ss_dssp             CCTTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEESCHHHHHHHH
T ss_pred             CCCCCEEEEEccCCCCCCCCeEEEEEEEcCCEEEEeC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeCcHHHHHHHH
Confidence            4567899999999873  33677766432 2222333 57899999999999999985    479999999999999998


Q ss_pred             cccC-----------CCCCcchhHHHHH-HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCCC
Q psy9180         222 NVSF-----------TNPLVSKVYSCWD-LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNP  274 (491)
Q Consensus       222 ~~~~-----------~~~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~  274 (491)
                      ++..           ..|...+++.+++ .+..+...|.|.|||||+|++|||.||+|||+|+..
T Consensus        83 ~w~~~W~~~gw~~~~g~~v~n~~l~~~l~~~l~~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~  147 (150)
T 3qio_A           83 QWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRK  147 (150)
T ss_dssp             HHHHHHCC------------CHHHHHHHHHHHTTCSEEEEEECCTTSCCHHHHHHHHHHHTTTSC
T ss_pred             HHHHHHhhcCcCcCcCcccccHHHHHHHHHHHhhcCceEEEEccCcCCChhHHHHHHHHHHHHHH
Confidence            7521           1111224455555 333467899999999999999999999999999875

>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease, hydrolase, magnesium, metal-binding; 1.60A {Chlorobaculum tepidum}

Probab=99.82  E-value=2.4e-21  Score=174.70  Aligned_cols=124  Identities=21%  Similarity=0.147  Sum_probs=90.4

Q ss_pred             CceEEEecCCCCCC--CceeEeee--CCeeeEe-ecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHhc
Q psy9180         148 NYTICYTDGSKTMN--TTSCAFSI--DDLISSS-QLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSN  222 (491)
Q Consensus       148 ~~i~IyTDGS~~~~--~vG~g~v~--~~~~~~~-~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~~  222 (491)
                      ..++||||||+..+  ..|+|++.  ++....+ .....+|++.||+.|++.||+.+.+  ..++.|+|||+++++.|.+
T Consensus         3 ~~i~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~~   80 (146)
T 3h08_A            3 KTITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYDPATTNNRMELMAAIKGLEALKE--PARVQLYSDSAYLVNAMNE   80 (146)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCSS--CCEEEEEESCHHHHHHHHS
T ss_pred             ceEEEEEecCCCCCCCceEEEEEEEECCeeEEeecCCCCCcHHHHHHHHHHHHHHhcCc--cCcEEEEeChHHHHHHHHH
Confidence            46899999998753  36777663  3322111 1124688999999999999999876  5899999999999999987


Q ss_pred             -cc-----------CCCCCcchhHHHHH-HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCCC
Q psy9180         223 -VS-----------FTNPLVSKVYSCWD-LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNP  274 (491)
Q Consensus       223 -~~-----------~~~~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~  274 (491)
                       +.           ...+...+++.+++ .+.. ...|.|.|||||+|++|||.||+|||+|+..
T Consensus        81 ~w~~~W~~~~w~~~~~~~v~n~~l~~~~~~~~~-~~~v~~~~V~gH~g~~~N~~AD~LA~~a~~~  144 (146)
T 3h08_A           81 GWLKRWVKNGWKTAAKKPVENIDLWQEILKLTT-LHRVTFHKVKGHSDNPYNSRADELARLAIKE  144 (146)
T ss_dssp             SHHHHHHHTTCC----CCCTTHHHHHHHHHHHH-HSEEEEEECCC-CCSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCccCCCCCcCCHHHHHHHHHHHh-hCceEEEEcCCcCCcHhHHHHHHHHHHHHHh
Confidence             21           01122224566666 2222 3579999999999999999999999998754

>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV, RNAse H, reverse transcriptase, transcription; 1.50A {Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A 3v1r_A* 2hb5_A 4e89_A

Probab=99.81  E-value=2.3e-20  Score=172.17  Aligned_cols=126  Identities=25%  Similarity=0.211  Sum_probs=93.9

Q ss_pred             CceEEEecCCCC--CCCceeEee--eCCe-eeEeecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHhc
Q psy9180         148 NYTICYTDGSKT--MNTTSCAFS--IDDL-ISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSN  222 (491)
Q Consensus       148 ~~i~IyTDGS~~--~~~vG~g~v--~~~~-~~~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~~  222 (491)
                      ..+.||||||+.  +|..|+|++  ..+. .....+...+|++.||+.|+..||+.+   ...++.|+|||+++++++-.
T Consensus        22 ~~i~iytDGs~~~npG~~g~G~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~---~~~~v~I~tDS~~vi~~iw~   98 (165)
T 3p1g_A           22 ADYTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA---EGKKLNVYTDSRYAFATAHV   98 (165)
T ss_dssp             CSEEEEEEEEEEEETTEEEEEEEEECSSCEEEEEEECTTCCHHHHHHHHHHHHHHHT---BTSEEEEEECCHHHHHHHHS
T ss_pred             CCEEEEEEcccCCCCCceEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHc---cCceEEEEEchHHHHhhhhc
Confidence            358999999997  344677754  2222 222245678899999999999999998   26899999999999999932


Q ss_pred             ccCCCCCcchhHHHHH-HhhcCCCeEEEEEeeccCC-----CCCChHHhHHhhCCCCCCC
Q psy9180         223 VSFTNPLVSKVYSCWD-LLRSRNKVVHFLWCPSHCG-----IRGNEAVDEAARNPVNPTQ  276 (491)
Q Consensus       223 ~~~~~~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~g-----i~gNE~AD~lAk~A~~~~~  276 (491)
                      .....+....+..+++ .....+..|.|.|||||+|     ++|||.||+|||+|+....
T Consensus        99 ~~~g~~v~n~dl~~~l~~~l~~~~~v~~~wVkgH~g~~~~~~~gNe~AD~LA~~aa~~~~  158 (165)
T 3p1g_A           99 HSEGREIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAV  158 (165)
T ss_dssp             CCCSCCCSSHHHHHHHHHHTTSBSEEEEEECCSSCCSCSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCcccCHHHHHHHHHHHhcCCceEEEEecCCCCCCcCcchHHHHHHHHHHHHHhcCC
Confidence            2222232234555665 3233678999999999999     9999999999999987654

>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO enzyme, structural genomics, protein structure initiative; NMR {Desulfitobacterium hafniense dcb-2} PDB: 2kw4_A

Probab=99.81  E-value=1.5e-21  Score=176.74  Aligned_cols=127  Identities=16%  Similarity=0.105  Sum_probs=92.2

Q ss_pred             CCCceEEEecCCCCCCCceeEeee--CCee--eEe-ec--CC--CccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHH
Q psy9180         146 YANYTICYTDGSKTMNTTSCAFSI--DDLI--SSS-QL--NP--VNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSA  216 (491)
Q Consensus       146 ~~~~i~IyTDGS~~~~~vG~g~v~--~~~~--~~~-~l--~~--~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsa  216 (491)
                      .++.+.||||||+.++..|+|++.  .+..  .+. ..  +.  .+|++.||+.|+..||+.+.+.+. ++.|+|||+.+
T Consensus         3 ~~~~i~iytDGs~~~g~~G~G~vi~~~g~~~~~~~~~~~~~~~~~~tNn~aEl~A~~~AL~~a~~~~~-~v~I~tDS~~i   81 (147)
T 2kq2_A            3 DRTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLGV-KIRILHDYAGI   81 (147)
T ss_dssp             TTSCCEEECCCCCBTTBCEEEEEEEETTEEEEEEEEECCCGGGGGTCTTHHHHHHHHHHHHHHHHHTC-CCCBSSCCSTH
T ss_pred             CCCeEEEEECCCCCCCCcEEEEEEEECCEEEEEEeccccccccccccHHHHHHHHHHHHHHHHHHCCC-eEEEEECcHHH
Confidence            457799999999999778999764  2222  222 22  22  368999999999999998876555 99999999988


Q ss_pred             HHHHhcccCCCCCcchhHHHHH--HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCCCCCC
Q psy9180         217 LAALSNVSFTNPLVSKVYSCWD--LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQL  277 (491)
Q Consensus       217 l~aL~~~~~~~~~~~~~~~~~I--~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~~~~  277 (491)
                      ...+.+.+.   .. .......  +++.....|.|.|||||+|++|||.||+|||+|+....+
T Consensus        82 ~~w~~~~w~---~~-~~~~~~~~~l~~~l~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  140 (147)
T 2kq2_A           82 AFWATGEWK---AK-NEFTQAYAKLMNQYRGIYSFEKVKAHSGNEFNDYVDMKAKSALGIRDL  140 (147)
T ss_dssp             HHHTTSSSS---CC-HHHHHHHHCGGGGGSTTCCBCCCCCCCCCHHHHHHHHHHHHHHTCCCT
T ss_pred             HHHHhCCCc---cC-CcchHHHHHHHHHhcCCeeEEEecCcCCCcchHHHHHHHHHHHhcccc
Confidence            877765432   11 1111222  122111289999999999999999999999999987654

>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability, hydrogen exchange, cooperativity, hydrolase; 1.30A {Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A 1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A 1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A 3aa5_X 1rbv_A ...

Probab=99.80  E-value=3.3e-20  Score=169.29  Aligned_cols=126  Identities=18%  Similarity=0.183  Sum_probs=94.0

Q ss_pred             CceEEEecCCCCC--CCceeEeee--CCeee--EeecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHh
Q psy9180         148 NYTICYTDGSKTM--NTTSCAFSI--DDLIS--SSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALS  221 (491)
Q Consensus       148 ~~i~IyTDGS~~~--~~vG~g~v~--~~~~~--~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~  221 (491)
                      ..+.||||||+..  +..|+|++.  .+...  +..+ ..+|++.||+.|+..||+.+.+  ..++.|+|||+++++.|.
T Consensus         3 ~~~~iytDGs~~~n~~~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~aL~~~~~--~~~v~I~tDS~~vi~~i~   79 (155)
T 1jl1_A            3 KQVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGY-TRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGIT   79 (155)
T ss_dssp             CCEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHH
T ss_pred             ceEEEEEccccCCCCCceEEEEEEEECCeEEEEecCC-CCCcHHHHHHHHHHHHHHHhCc--CCcEEEEeCHHHHHHHHH
Confidence            3588999999984  336788764  23221  2222 4678999999999999999876  379999999999999999


Q ss_pred             ccc---------CC--CCCcchhHHHHH-HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCCCCCC
Q psy9180         222 NVS---------FT--NPLVSKVYSCWD-LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQL  277 (491)
Q Consensus       222 ~~~---------~~--~~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~~~~  277 (491)
                      ++.         ..  .|....++.+.| .+. ....|.|.|||||+|++|||.||+|||+|+..+.+
T Consensus        80 ~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~-~~~~v~~~wV~gH~g~~~Ne~AD~LA~~a~~~~~~  146 (155)
T 1jl1_A           80 QWIHNWKKRGWKTADKKPVKNVDLWQRLDAAL-GQHQIKWEWVKGHAGHPENERADELARAAAMNPTL  146 (155)
T ss_dssp             TTHHHHHHTTTBCTTSCBCTTHHHHHHHHHHT-TTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCB
T ss_pred             HHHHHHhhcccccccCCccCCHHHHHHHHHHH-ccCceEEEEcCCCCCCHHHHHHHHHHHHHHhccch
Confidence            721         11  121224556666 332 34689999999999999999999999999987654

>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A {Shewanella oneidensis} PDB: 2zqb_A

Probab=99.79  E-value=5.8e-20  Score=168.21  Aligned_cols=123  Identities=20%  Similarity=0.219  Sum_probs=91.7

Q ss_pred             CceEEEecCCCCC--CCceeEeee--CCeee--EeecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHh
Q psy9180         148 NYTICYTDGSKTM--NTTSCAFSI--DDLIS--SSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALS  221 (491)
Q Consensus       148 ~~i~IyTDGS~~~--~~vG~g~v~--~~~~~--~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~  221 (491)
                      ..+.||||||+..  +..|+|++.  .+...  +..+ ..+|++.||+.|+..||+.+.+  ..++.|+|||+++++.|.
T Consensus         5 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~-~~~tn~~aEl~A~~~AL~~~~~--~~~v~I~tDS~~vi~~i~   81 (158)
T 2e4l_A            5 KLIHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGF-SLTTNNRMELLAPIVALEALKE--PCKIILTSDSQYMRQGIM   81 (158)
T ss_dssp             CEEEEEEEEEESSSSEEEEEEEEEEETTEEEEEEEEE-EEECHHHHHHHHHHHHHHTCSS--CCEEEEEECCHHHHHHHH
T ss_pred             CeEEEEEcccccCCCCcEEEEEEEEECCEEEEEecCc-CCCccHHHHHHHHHHHHHHhcc--CCeEEEEeCHHHHHHHHH
Confidence            4689999999984  346788764  33221  1222 3578999999999999999865  389999999999999998


Q ss_pred             cc--------c-CCC--CCcchhHHHHH-HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCCC
Q psy9180         222 NV--------S-FTN--PLVSKVYSCWD-LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNP  274 (491)
Q Consensus       222 ~~--------~-~~~--~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~  274 (491)
                      ++        + ...  +....++.+.| .+. ....|.|.|||||+|++|||.||+|||+|+..
T Consensus        82 ~w~~~W~~n~~~~~~g~~v~n~~l~~~i~~l~-~~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~  145 (158)
T 2e4l_A           82 TWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAA-QLHQIDWRWVKGHAGHAENERCDQLARAAAEA  145 (158)
T ss_dssp             THHHHHHHTTTBCTTSSBCTTHHHHHHHHHHH-TTSEEEEEECCTTCCCHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHccccccCCCcccCHHHHHHHHHHH-ccCcEEEEEccCCCCchhHHHHHHHHHHHHHh
Confidence            82        1 111  11223455666 332 34689999999999999999999999999976

>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A

Probab=99.78  E-value=6.6e-20  Score=169.30  Aligned_cols=126  Identities=19%  Similarity=0.114  Sum_probs=93.1

Q ss_pred             CceEEEecCCCCC--CCceeEeeeC--CeeeEee-cCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHhc
Q psy9180         148 NYTICYTDGSKTM--NTTSCAFSID--DLISSSQ-LNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSN  222 (491)
Q Consensus       148 ~~i~IyTDGS~~~--~~vG~g~v~~--~~~~~~~-l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~~  222 (491)
                      ..+.||||||+..  +..|+|++..  +....+. ....+|++.||+.|++.||+.+.+.  .++.|+|||+++++.|.+
T Consensus         7 ~~i~iytDGs~~~n~g~~G~G~v~~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~~--~~v~I~tDS~~vi~~i~~   84 (166)
T 1ril_A            7 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEP--CEVDLYTDSHYLKKAFTE   84 (166)
T ss_dssp             CCCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCSC--CEEEEECCCHHHHHHHHS
T ss_pred             ccEEEEECccccCCCCCEEEEEEEEECCEEEEEecCCCCCcHHHHHHHHHHHHHHHhccC--CeEEEEeChHHHHHHHhh
Confidence            5689999999984  3467887643  2211111 1246789999999999999988653  599999999999999998


Q ss_pred             ----------ccCCC--CCcchhHHHHH-HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCCCCC
Q psy9180         223 ----------VSFTN--PLVSKVYSCWD-LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQ  276 (491)
Q Consensus       223 ----------~~~~~--~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~~~  276 (491)
                                +....  +...+++.++| .+.. ...|.|.|||||+|++|||.||+|||+|+....
T Consensus        85 ~w~~~W~~~~w~~~~g~~v~n~~l~~~i~~l~~-~~~v~~~wV~gH~g~~~Ne~AD~LAk~a~~~~~  150 (166)
T 1ril_A           85 GWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMA-PHRVRFHFVKGHTGHPENERVDREARRQAQSQA  150 (166)
T ss_dssp             SHHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHT-TSEEECCCCCGGGSCTHHHHHHHHHHHHHTSSC
T ss_pred             hHHHHHHhcccccccCCccCcHHHHHHHHHHHh-cCeEEEEEeeCCCCchhHHHHHHHHHHHHHHhh
Confidence                      22111  11224566666 3332 469999999999999999999999999987754

>2lsn_A Reverse transcriptase; RNAse H, viral protein; NMR {Simian foamy virus}

Probab=99.74  E-value=1.5e-18  Score=160.02  Aligned_cols=126  Identities=15%  Similarity=0.069  Sum_probs=89.7

Q ss_pred             CCceEEEecCCCCC--CC-----ceeEeeeC--C----eeeEeec-CCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcc
Q psy9180         147 ANYTICYTDGSKTM--NT-----TSCAFSID--D----LISSSQL-NPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSD  212 (491)
Q Consensus       147 ~~~i~IyTDGS~~~--~~-----vG~g~v~~--~----~~~~~~l-~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tD  212 (491)
                      ...++||||||+..  |+     .|+|++..  +    ....+.. ....+.+.||+.|+..||+.+... ..+|.|+||
T Consensus         5 ~~evviYTDGsc~gNpgp~~~~~aG~Gv~~~~~~~~~~~~~~~~~~tnn~te~~Aei~Al~~al~~al~~-~~~v~I~TD   83 (165)
T 2lsn_A            5 QYEGVFYTDGSAIKSPDPTKSNNAGMGIVHATYKPEYQVLNQWSIPLGNHTAQMAEIAAVEFACKKALKI-PGPVLVITD   83 (165)
T ss_dssp             CCSEEEEEEEEEEECSSCTTCEEEEEEEEEECCSSSCCEEEEEEEEESSCCHHHHHHHHHHHHHHHHHHS-SSCEEEEES
T ss_pred             CceEEEEEcCCCCCCCCCCCCCcEEEEEEEEECCCccEEeccccCCchHHHHHHHHHHHHHHHHHHHhcC-CCeEEEEeC
Confidence            45678999999883  22     68887632  1    1223333 356788889999999999887663 357999999


Q ss_pred             cHHHHHHHhcccC-----------CCCCcchhHHHHH-HhhcCCCeEEEEEeeccCCC------CCChHHhHHhhCCCC
Q psy9180         213 SRSALAALSNVSF-----------TNPLVSKVYSCWD-LLRSRNKVVHFLWCPSHCGI------RGNEAVDEAARNPVN  273 (491)
Q Consensus       213 Sqsal~aL~~~~~-----------~~~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi------~gNE~AD~lAk~A~~  273 (491)
                      |+++++++..+..           +.|....++.+++ .+......|.|.|||||+|+      +|||.||+||++|+.
T Consensus        84 S~Yvi~~it~w~~~Wk~ngw~~~~~~pVkN~dL~~~l~~~~~~~~~v~~~~VkgH~g~~~~~~~~gNe~AD~LA~~gA~  162 (165)
T 2lsn_A           84 SFYVAESANKELPYWKSNGFVNNKKKPLKHISKWKSIAECLSMKPDITIQHEKGHQPTNTSIHTEGNALADKLATQGSY  162 (165)
T ss_dssp             CHHHHHHHHTHHHHHHHTTSCSCSSSCCSSHHHHHHHHHHHHHCTTCEEEECCSSSCSSSCHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHhhhhhhhhhheeccccccCCCcccCHHHHHHHHHHHhCCCCEEEEEEeCCCCccCCCCChHHHHHHHHHHHhhh
Confidence            9999999975321           1122234566666 33344568999999999995      579999999999864

>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B

Probab=99.69  E-value=3.9e-17  Score=177.47  Aligned_cols=118  Identities=20%  Similarity=0.254  Sum_probs=90.0

Q ss_pred             CCceEEEecCCCCC-CC-ceeEeeeCC-eeeEeecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHhcc
Q psy9180         147 ANYTICYTDGSKTM-NT-TSCAFSIDD-LISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNV  223 (491)
Q Consensus       147 ~~~i~IyTDGS~~~-~~-vG~g~v~~~-~~~~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~~~  223 (491)
                      ++.+.||||||+.. ++ .|+|++... ......+ ..+|++.||+.|+..||+.    ...++.|+|||++|++++.++
T Consensus       434 ~~~~~iytDGs~~~n~g~~g~G~v~~~~~~~~~~~-~~~TNn~aEl~A~i~aL~~----~~~~v~I~tDS~~v~~~i~~~  508 (555)
T 1mu2_A          434 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQ  508 (555)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTC
T ss_pred             CCceEEEEcccccCCCCCceEEEEEEeCCEeeccC-CCCCHHHHHHHHHHHHHHc----CCCeEEEEEehHHHHHHHhcc
Confidence            56799999999874 33 567766432 2222222 4678999999999999998    467999999999999999985


Q ss_pred             cCCCCCcchhHHHHH-HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCC
Q psy9180         224 SFTNPLVSKVYSCWD-LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPV  272 (491)
Q Consensus       224 ~~~~~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~  272 (491)
                      ...   ..+.+.+++ .+...+..|.|.|||||+|++|||.||+|||+|+
T Consensus       509 ~~~---~~~~l~~~~~~~~~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a~  555 (555)
T 1mu2_A          509 PTE---SESKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  555 (555)
T ss_dssp             CSE---ESCHHHHHHHHHHHHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             ccc---ccHHHHHHHHHHhccCCcEEEEEEECCCCChhHHHHHHHHHhhC
Confidence            431   124455555 3333467899999999999999999999999985

>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 3is9_A* 3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ...

Probab=99.69  E-value=3.5e-17  Score=177.86  Aligned_cols=117  Identities=24%  Similarity=0.284  Sum_probs=86.7

Q ss_pred             CCceEEEecCCCC-CCC-ceeEeeeCC-eeeEeecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHhcc
Q psy9180         147 ANYTICYTDGSKT-MNT-TSCAFSIDD-LISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNV  223 (491)
Q Consensus       147 ~~~i~IyTDGS~~-~~~-vG~g~v~~~-~~~~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~~~  223 (491)
                      .+.+.||||||+. +++ .|+|++..+ ....... ..+|++.||+.|++.||+.+    ..++.|+|||++|++++.++
T Consensus       437 ~~~~~iytDGs~~~n~g~~g~g~v~~~~~~~~~~~-~~~TNn~aEl~Ai~~aL~~~----~~~v~I~tDS~~vi~~i~~~  511 (557)
T 2zd1_A          437 VGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPL-TNTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQAQ  511 (557)
T ss_dssp             TTSCEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-CSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHTTC
T ss_pred             CCCEEEEEccCCCCCCCceEEEEEEECCcEEEecC-CCCCHHHHHHHHHHHHHHhC----CCcEEEEeChHHHHHHHhcC
Confidence            4669999999987 333 566766432 2222232 46899999999999999998    57999999999999999986


Q ss_pred             cCCCCCcchhHHHHH-HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCC
Q psy9180         224 SFTNPLVSKVYSCWD-LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNP  271 (491)
Q Consensus       224 ~~~~~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A  271 (491)
                      ..++   .+++.+++ ........|.|.|||||+|++|||.||+|||+|
T Consensus       512 ~~~~---~~~l~~~~~~~l~~~~~v~~~wV~~H~g~~~Ne~AD~LA~~a  557 (557)
T 2zd1_A          512 PDKS---ESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAG  557 (557)
T ss_dssp             CSEE---SSHHHHHHHHHHHHCSEEEEEECCSSSCCTTCCGGGGCC---
T ss_pred             CccC---CHHHHHHHHHHHhcCCCEEEEEcCCCCCChhHHHHHHHHhcC
Confidence            5321   24455555 222234689999999999999999999999986

>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal domain, fusion protein, maltose binding protein, HYDR; HET: MLR TAR; 2.25A {Mycobacterium tuberculosis}

Probab=99.68  E-value=2.6e-17  Score=146.49  Aligned_cols=119  Identities=15%  Similarity=0.164  Sum_probs=88.8

Q ss_pred             ceEEEecCCCCC--CCceeEeee--CC---eeeEe-ecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHH
Q psy9180         149 YTICYTDGSKTM--NTTSCAFSI--DD---LISSS-QLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAAL  220 (491)
Q Consensus       149 ~i~IyTDGS~~~--~~vG~g~v~--~~---~~~~~-~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL  220 (491)
                      .++||||||+..  +..|+|++.  .+   ....+ .....+|++.||+.|++.||+.+.+.+..++.|+|||+++++.+
T Consensus         3 ~~~iy~DGs~~~~~g~~g~G~v~~~~~~~~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~~~~~v~i~tDS~~vv~~i   82 (141)
T 3hst_B            3 KVVIEADGGSRGNPGPAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQM   82 (141)
T ss_dssp             EEEEEEEEEESSSSEEEEEEEEEEETTSCSEEEEEEEEEEEECHHHHHHHHHHHHHHHHHHHTCSEEEEEESCHHHHHHH
T ss_pred             EEEEEEecCCCCCCCCcEEEEEEEeCCCCcEEEeeeccCCCCchHHHHHHHHHHHHHHHHHCCCceEEEEeChHHHHHHH
Confidence            479999999884  357888663  22   11111 12247899999999999999999987788999999999999999


Q ss_pred             hcccCCCCCcchh---HHHHH-HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCCC
Q psy9180         221 SNVSFTNPLVSKV---YSCWD-LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNP  274 (491)
Q Consensus       221 ~~~~~~~~~~~~~---~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~  274 (491)
                      .+.+.   .....   +.+++ .+..+...|.|.|||+    ++|+.||+|||+|+..
T Consensus        83 ~~~~~---~~~~~l~~~~~~i~~l~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~~  133 (141)
T 3hst_B           83 SGRWK---VKHPDLLKLYVQAQALASQFRRINYEWVPR----ARNTYADRLANDAMDA  133 (141)
T ss_dssp             TTSSC---CCSHHHHHHHHHHHHHHTTSSEEEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             hCCcc---cCCHHHHHHHHHHHHHHhcCCeEEEEEcCC----cccHHHHHHHHHHHHH
Confidence            97431   11122   23344 4455568999999995    8999999999988753

>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of RNA/DNA hybrid; 1.40A {Uncultured organism}

Probab=99.68  E-value=1.7e-17  Score=146.99  Aligned_cols=121  Identities=21%  Similarity=0.194  Sum_probs=87.7

Q ss_pred             CceEEEecCCCCC--CCceeEeeeC--C--ee-eEeecCCCccchHHHHHHHHHHHHHHHcCCCC----eEEEEcccHHH
Q psy9180         148 NYTICYTDGSKTM--NTTSCAFSID--D--LI-SSSQLNPVNSIFSAELIAIYLCLEAITVHPSD----QFLIVSDSRSA  216 (491)
Q Consensus       148 ~~i~IyTDGS~~~--~~vG~g~v~~--~--~~-~~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~----~i~I~tDSqsa  216 (491)
                      ..++||||||+..  +..|+|++..  +  .. ........+|++.||+.|+..||+.+.+.+.+    ++.|+|||+++
T Consensus         2 ~~~~iy~DGs~~~n~g~~G~G~v~~~~~g~~~~~~~~~~~~~tn~~aEl~A~~~aL~~a~~~~~~~~~~~v~i~tDS~~v   81 (140)
T 3u3g_D            2 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQMFGDKLVDMEVEVRMDSELI   81 (140)
T ss_dssp             CEEEEEEEEEESSTTEEEEEEEEEECTTSCEEEEEEEEEEEECHHHHHHHHHHHHHHHHGGGGGGGTTCEEEEEESCHHH
T ss_pred             ceEEEEEecCCCCCCCCcEEEEEEEeCCCCEEEEEEeeCCCCchHHHHHHHHHHHHHHHHHcCCCCCCceEEEEeChHHH
Confidence            3589999999974  3478887642  2  11 11122235799999999999999999876666    99999999999


Q ss_pred             HHHHhcccC-CCCCcchhHHHHH-Hh-hcCCCeEEEEEeeccCCCCCChHHhHHhhCCCC
Q psy9180         217 LAALSNVSF-TNPLVSKVYSCWD-LL-RSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVN  273 (491)
Q Consensus       217 l~aL~~~~~-~~~~~~~~~~~~I-~l-~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~  273 (491)
                      ++.+.+.+. +++ .-..+.+++ .+ ..+...|.|.|||+    ++||.||+|||+|+.
T Consensus        82 i~~i~~~~~~~~~-~l~~~~~~i~~l~~~~~~~v~~~~V~~----~~N~~AD~LA~~a~~  136 (140)
T 3u3g_D           82 VRQMQGVYKVKEP-TLKEKFAKIAHIKMERVPNLVFVHIPR----EKNARADELVNEAID  136 (140)
T ss_dssp             HHHHTTSSCCCCG-GGHHHHHHHHHHHHHHCTTCEEEECCG----GGGHHHHHHHHHHHH
T ss_pred             HHHhCCCcccCCH-HHHHHHHHHHHHhhcCCCcEEEEEcCc----hhhHHHHHHHHHHHH
Confidence            999998542 111 112234445 34 44446899999994    899999999998864

>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus tokodaii} PDB: 3aly_A

Probab=99.65  E-value=1.2e-16  Score=144.17  Aligned_cols=120  Identities=17%  Similarity=0.125  Sum_probs=87.5

Q ss_pred             eEEEecCCCC--C-CCcee-EeeeC-C--eeeEee--cC---CCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHH
Q psy9180         150 TICYTDGSKT--M-NTTSC-AFSID-D--LISSSQ--LN---PVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSAL  217 (491)
Q Consensus       150 i~IyTDGS~~--~-~~vG~-g~v~~-~--~~~~~~--l~---~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal  217 (491)
                      +.||||||+.  + +..|+ |++.. +  ....+.  +.   ..+|++.||+.|+..||+.+.+.+..++.|+|||+.++
T Consensus         2 ~~iy~DGs~~~~n~g~~G~~G~vi~~~g~~~~~~~~~~~~~~~~~tnn~aEl~A~~~aL~~a~~~g~~~v~i~tDS~~vi   81 (149)
T 2ehg_A            2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVI   81 (149)
T ss_dssp             CEEEEEEEEESSSSSSEEEEEEEEECSSCEEEEEEECSCTTCTTCCHHHHHHHHHHHHHHHHHHHTCCSCEEEESCHHHH
T ss_pred             EEEEEeeccCCCCCChheEEEEEEEECCEEEEEeccccCCCCCCccHHHHHHHHHHHHHHHHHHcCCCEEEEEeChHHHH
Confidence            6899999987  2 55775 76532 2  222222  22   37899999999999999999987778999999999999


Q ss_pred             HHHhcccCCCCCcchhHHHHH-HhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCCC
Q psy9180         218 AALSNVSFTNPLVSKVYSCWD-LLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNP  274 (491)
Q Consensus       218 ~aL~~~~~~~~~~~~~~~~~I-~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~  274 (491)
                      +.+.+++..+......+.+++ .+.... .|.|.|||+    ++|+.||+|||+|+..
T Consensus        82 ~~i~~~w~~~~~~~~~l~~~i~~l~~~~-~v~~~~V~~----~~N~~AD~LA~~a~~~  134 (149)
T 2ehg_A           82 KQMNGEYKVKAKRIIPLYEKAIELKKKL-NATLIWVPR----EENKEADRLSRVAYEL  134 (149)
T ss_dssp             HHHTTSSCCCCTTHHHHHHHHHHHHHHH-TCEEEECCG----GGCHHHHHHHHHHHHH
T ss_pred             HHHhCccccCCHHHHHHHHHHHHHHhcC-CEEEEEcCC----cccHHHHHHHHHHHHh
Confidence            999987432211224455555 222222 499999998    4999999999998754

>1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE motif, hydrolase; 1.50A {Bacillus halodurans} SCOP: c.55.3.1 PDB: 1zbi_A 2g8u_A 2g8i_A 2g8h_A 2g8k_A 2g8f_A 2g8v_A 2g8w_A 3ey1_A* 1zbl_A 3d0p_A* 3i8d_A* 2r7y_A*

Probab=99.08  E-value=2.4e-11  Score=109.06  Aligned_cols=120  Identities=11%  Similarity=-0.066  Sum_probs=83.5

Q ss_pred             CCCceEEEecCCCCC--CCceeEeeeCC--eeeEeec-CCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHH
Q psy9180         146 YANYTICYTDGSKTM--NTTSCAFSIDD--LISSSQL-NPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAAL  220 (491)
Q Consensus       146 ~~~~i~IyTDGS~~~--~~vG~g~v~~~--~~~~~~l-~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL  220 (491)
                      .+..+.||||||+..  |..|+|++...  .....+. -..+|++.||+.|++.||+.+.+... ++.|+|||+.+++.+
T Consensus         8 ~~~~~~iy~DGa~~gNpG~~G~G~vl~~~g~~~~~~~~~~~~TNN~aEl~A~i~aL~~~~~~~~-~v~i~tDS~~vi~w~   86 (142)
T 1zbf_A            8 EIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNS-RKPIYSNSQTAIKWV   86 (142)
T ss_dssp             CCCSSSEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTTC-CCCEEESCHHHHHHH
T ss_pred             CCCeEEEEEeeccCCCCCCeEEEEEEEeCCEEEEEecccCCcCcHHHHHHHHHHHHHHHHhCCC-eEEEEEehHHHHHHH
Confidence            456789999999873  44788877532  1111111 12578999999999999999998666 899999999999999


Q ss_pred             hcccCCC----CCcchhHHHHH-Hh--hcCCCeEEEEEeeccCCCCCChHHhH
Q psy9180         221 SNVSFTN----PLVSKVYSCWD-LL--RSRNKVVHFLWCPSHCGIRGNEAVDE  266 (491)
Q Consensus       221 ~~~~~~~----~~~~~~~~~~I-~l--~~~~~~V~~~WVPgH~gi~gNE~AD~  266 (491)
                      ++...+.    +....++.+.+ .+  -.+...+....|+-|++.-||.-||.
T Consensus        87 ~~~~~k~~~~~~v~n~dLw~~l~~~~~w~~~~~~~~~~~kw~~~~~ge~pad~  139 (142)
T 1zbf_A           87 KDKKAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKADY  139 (142)
T ss_dssp             HHTCCCCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTCC
T ss_pred             HcCCccCCCCCCcccHHHHHHHHHHHHHHhhCCCceeEEEeccCccCcCcccc
Confidence            9876321    11223455555 11  12334566667788988899999984

>4htu_A Ribonuclease H, RNAse H; 5-chloro-2'-deoxyuridine, W-C base PAIR, wobble base PAIR, D helix; HET: DNA UCL; 1.49A {Bacillus halodurans} PDB: 3d0p_A* 4hue_A* 4huf_A* 4hug_A* 1zbf_A 1zbi_A 2g8u_A 3uld_A* 3ey1_A* 3twh_A* 2g8f_A 2g8v_A 2g8w_A 2g8i_A 2g8h_A 2g8k_A 3i8d_A* 2r7y_A* 1zbl_A

Probab=98.77  E-value=5.3e-09  Score=92.57  Aligned_cols=76  Identities=14%  Similarity=0.077  Sum_probs=56.4

Q ss_pred             CCceEEEecCCCCC--CCceeEeee-CC-e-e-eEeecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHH
Q psy9180         147 ANYTICYTDGSKTM--NTTSCAFSI-DD-L-I-SSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAAL  220 (491)
Q Consensus       147 ~~~i~IyTDGS~~~--~~vG~g~v~-~~-~-~-~~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL  220 (491)
                      +....||||||+..  |..|+|+|. .+ . . ....+ ..+|++.||++|++.||+.+.+.+.. +.|+|||++|++.+
T Consensus         3 p~~~~iytDGac~GNPGp~G~ggV~~~~g~~~~~~g~~-~~tTNN~aEl~A~i~aL~~l~~~~~~-v~i~tDSqyVi~wi   80 (134)
T 4htu_A            3 IIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPI-PIGTNNMGEFLAIVHGLRYLKERNSR-KPIYSNSQTAIKWV   80 (134)
T ss_dssp             CCSSSEEEEEEEETTTEEEEEEEEETTTCCEEEEEEEE-EEECHHHHHHHHHHHHHHHHHHTTCC-CCEEESCHHHHHHH
T ss_pred             ccceEEEEeeccCCCCCCeEEEEEEEECCEEEEEecCC-CCCchHHHHHHHHHHHHHHHHhCCCC-EEEEcchHHHHHHH
Confidence            45678999999873  346775443 22 1 1 12222 36899999999999999999875444 89999999999999


Q ss_pred             hccc
Q psy9180         221 SNVS  224 (491)
Q Consensus       221 ~~~~  224 (491)
                      .+..
T Consensus        81 ~~~~   84 (134)
T 4htu_A           81 KDKK   84 (134)
T ss_dssp             HHTC
T ss_pred             HcCC
Confidence            8754

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	491
d1mu2a1	126	c.55.3.1 (A:430-555) HIV RNase H (Domain of revers	3e-07
d1rila_	147	c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermoph	5e-05
d1jl1a_	152	c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli	5e-04

>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]} Length = 126

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 2 [TaxId: 11709]

 Score = 47.2 bits (111), Expect = 3e-07
 Identities = 25/119 (21%), Positives = 46/119 (38%), Gaps = 8/119 (6%)

Query: 153 YTDGSKTMNTT--SCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIV 210
           YTDGS    +      +  D      +     +   AEL A  + L         +  I+
Sbjct: 11  YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALT----DSGPKVNII 66

Query: 211 SDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDEAAR 269
            DS+  +  +++    +   SK+ +       + + ++  W P+H GI GN+ VD    
Sbjct: 67  VDSQYVMGIVASQPTESE--SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVS 123

>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]} Length = 147

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Thermus thermophilus [TaxId: 274]

 Score = 41.1 bits (95), Expect = 5e-05
 Identities = 25/133 (18%), Positives = 42/133 (31%), Gaps = 15/133 (11%)

Query: 153 YTDGSKTMNTTSCAFSI-----DDLISSSQLNPVNSIFSAELIAIYLCLEA------ITV 201
           +TDG+   N     ++            S      +    EL A    L+A      + +
Sbjct: 7   FTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPCEVDL 66

Query: 202 HPSDQFLIVSDSRSAL----AALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCG 257
           +    +L  + +   L          +   P+ ++      LL      V F +   H G
Sbjct: 67  YTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTG 126

Query: 258 IRGNEAVDEAARN 270
              NE VD  AR 
Sbjct: 127 HPENERVDREARR 139

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]} Length = 152

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Escherichia coli [TaxId: 562]

 Score = 38.5 bits (88), Expect = 5e-04
 Identities = 24/131 (18%), Positives = 39/131 (29%), Gaps = 14/131 (10%)

Query: 153 YTDGSKTMNTTSCAFSI-----DDLISSSQLNPVNSIFSAELIAIYLCLEA------ITV 201
           +T GS   N     +           + S      +    EL+A  + LEA      + +
Sbjct: 6   FTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAEVIL 65

Query: 202 HPSDQFLIVSDSRSALAALSNVS-FTNPLVSKVYSCWDLLR--SRNKVVHFLWCPSHCGI 258
               Q++    ++             +    K    W  L        + + W   H G 
Sbjct: 66  STDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGH 125

Query: 259 RGNEAVDEAAR 269
             NE  DE AR
Sbjct: 126 PENERADELAR 136

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	491
d1mu2a1	126	HIV RNase H (Domain of reverse transcriptase) {Hum	99.87
d1jl1a_	152	RNase H (RNase HI) {Escherichia coli [TaxId: 562]}	99.82
d1rila_	147	RNase H (RNase HI) {Thermus thermophilus [TaxId: 2	99.82
d1s1ta1	110	HIV RNase H (Domain of reverse transcriptase) {Hum	99.62
d1zbfa1	132	BH0863-like Ribonuclease H {Bacillus halodurans [T	99.33

>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 2 [TaxId: 11709]

Probab=99.87  E-value=1e-22  Score=177.34  Aligned_cols=119  Identities=22%  Similarity=0.284  Sum_probs=87.7

Q ss_pred             CCceEEEecCCCC-CCC-ceeEeeeCCe-eeEeecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHhcc
Q psy9180         147 ANYTICYTDGSKT-MNT-TSCAFSIDDL-ISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNV  223 (491)
Q Consensus       147 ~~~i~IyTDGS~~-~~~-vG~g~v~~~~-~~~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~~~  223 (491)
                      ++..++|||||+. +++ .|+|++.... .....+ ..+|++.|||.||.+||+.    ...++.|+|||++++..+.+.
T Consensus         5 ~~~~t~YTDGS~~~n~~~~~~g~~~~~~~~~~~~~-~~~tnn~AEl~Ai~~al~~----~~~~i~I~tDS~~v~~~~~~~   79 (126)
T d1mu2a1           5 PGAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKL-EQTTNQQAELEAFAMALTD----SGPKVNIIVDSQYVMGIVASQ   79 (126)
T ss_dssp             TTCEEEEEEEEECTTTCCEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHT----SCSEEEEEESCHHHHHHHHTC
T ss_pred             CCCcEEEEcCCCCCCCCcEEEEEEecCCCEEEEec-CCCcchHHHHHHHHHHhcc----CCcceEEEechHHHHHHHhcC
Confidence            4667899999976 444 4455554432 223333 3579999999999999985    357899999999999999986


Q ss_pred             cCCCCCcchhHHHHHHhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCC
Q psy9180         224 SFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPV  272 (491)
Q Consensus       224 ~~~~~~~~~~~~~~I~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~  272 (491)
                      ...+.  ...+.+.+........|.|.|||||+|++|||.||+|||+|+
T Consensus        80 ~~~~~--~~~~~~~~~~~~~~~~v~~~wV~gH~g~~gNe~AD~LA~~ai  126 (126)
T d1mu2a1          80 PTESE--SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQGI  126 (126)
T ss_dssp             CSEES--CHHHHHHHHHHHHCSEEEEEECCSSSCCTTHHHHHHHHHTTC
T ss_pred             Ccccc--chHHHHHHHHhhhcceeEEEEEeCCCCCcchHHHHHHHHhhC
Confidence            54221  122333343333456899999999999999999999999985

>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Escherichia coli [TaxId: 562]

Probab=99.82  E-value=3.6e-21  Score=171.72  Aligned_cols=132  Identities=17%  Similarity=0.151  Sum_probs=95.5

Q ss_pred             ceEEEecCCCCCC--CceeEeee--CCeeeEeec-CCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHhcc
Q psy9180         149 YTICYTDGSKTMN--TTSCAFSI--DDLISSSQL-NPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNV  223 (491)
Q Consensus       149 ~i~IyTDGS~~~~--~vG~g~v~--~~~~~~~~l-~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~~~  223 (491)
                      .|.||||||+.++  ..|+|++.  .+....+.. ....|++.||+.|+..||+.+..  ...+.|++||++++..+...
T Consensus         2 ~I~IYtDGS~~~N~g~aG~G~vi~~~~~~~~~~~~~~~~tnn~aE~~Ai~~Al~~~~~--~~~i~i~tds~~~i~~~~~~   79 (152)
T d1jl1a_           2 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKE--HAEVILSTDSQYVRQGITQW   79 (152)
T ss_dssp             CEEEEEEEEESSTTEEEEEEEEEEETTEEEEEEEEEEEECHHHHHHHHHHHHHHTCCS--CCEEEEEECCHHHHHHHHTT
T ss_pred             EEEEEEeCCCCCCCCcEEEEEEEEECCeEEEeccccCcccHHHHHHhhhhhhhhhhcc--cceEEEeecceeeEEcccch
Confidence            4899999998743  36778653  443332222 34578999999999999998654  57899999999999988754


Q ss_pred             cCC---------C--CCcchhHHHHHHhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCCCCCCCCCCc
Q psy9180         224 SFT---------N--PLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQLKLCSP  282 (491)
Q Consensus       224 ~~~---------~--~~~~~~~~~~I~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~~~~~~~~~  282 (491)
                      ...         .  +....++.+.+........|+|+|||||+|++|||.||+|||+|+..+.+.+.++
T Consensus        80 ~~~~~~~~~~~~~~~~~~n~~~~~~i~~~~~~~~V~~~wV~gH~g~~gNe~AD~LAk~aa~~~~~~d~~~  149 (152)
T d1jl1a_          80 IHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLEDTGY  149 (152)
T ss_dssp             HHHHHHTTTBCTTSCBCTTHHHHHHHHHHTTTCEEEEEECCSSTTCHHHHHHHHHHHHHHHSCCBCCTTC
T ss_pred             hhHhHhccchhcccCeeecHHHHHHHHHHhhcceeEEEEecccCCCccHHHHHHHHHHHHhCCCCCccCC
Confidence            311         0  1111223444422335678999999999999999999999999999887766555

>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: RNase H (RNase HI)
species: Thermus thermophilus [TaxId: 274]

Probab=99.82  E-value=1.5e-21  Score=174.05  Aligned_cols=125  Identities=22%  Similarity=0.140  Sum_probs=90.2

Q ss_pred             ceEEEecCCCCCC--CceeEeee--CCe-eeEeecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHhcc
Q psy9180         149 YTICYTDGSKTMN--TTSCAFSI--DDL-ISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNV  223 (491)
Q Consensus       149 ~i~IyTDGS~~~~--~vG~g~v~--~~~-~~~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~~~  223 (491)
                      .++||||||+.++  ..|+|++.  .+. ...+.....+|++.||+.|+..||+.+..  ...+.|++||++++..+...
T Consensus         3 ~i~iytDGs~~~N~g~~G~g~vi~~~~~~~~~~~~~~~~Tnn~aEl~Ai~~AL~~~~~--~~~i~i~tds~~~~~~~~~~   80 (147)
T d1rila_           3 RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE--PCEVDLYTDSHYLKKAFTEG   80 (147)
T ss_dssp             CCCEEEEEEESSTTEEEEEEEEECBTTBCCEECCEEEEECHHHHHHHHHHHHHHSCCS--CCEEEEECCCHHHHHHHHSS
T ss_pred             EEEEEEccCCCCCCCccEEEEEEEECCcceEEecccccccHHHHHHHHHHHHhhhccC--CceEEEecchhhhhcccccc
Confidence            5889999998853  35777653  222 22222234568999999999999987643  57899999999999988653


Q ss_pred             cCC------------CCCcchhHHHHHHhhcCCCeEEEEEeeccCCCCCChHHhHHhhCCCCCC
Q psy9180         224 SFT------------NPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPT  275 (491)
Q Consensus       224 ~~~------------~~~~~~~~~~~I~l~~~~~~V~~~WVPgH~gi~gNE~AD~lAk~A~~~~  275 (491)
                      ...            .|....++.+++........|+|.|||||+|++|||.||+|||+|++..
T Consensus        81 ~~~~~~~~~~~~~~~~~v~n~dL~~~l~~~~~~~~v~~~wVkgHsg~~gNe~AD~LAk~aa~~~  144 (147)
T d1rila_          81 WLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQ  144 (147)
T ss_dssp             HHHHHHHTTSBCTTSSBCTTHHHHHHHHHHHTTSEEECCCCCGGGSCTHHHHHHHHHHHHHTSS
T ss_pred             chhhhhhccccccccccchhHHHHHHHHHHhhhcccceEEccCCCCCcchHHHHHHHHHHHHHh
Confidence            210            1111234556663334567899999999999999999999999998764

>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 1 [TaxId: 11676]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: HIV RNase H (Domain of reverse transcriptase)
species: Human immunodeficiency virus type 1 [TaxId: 11676]

Probab=99.62  E-value=4.3e-16  Score=132.12  Aligned_cols=102  Identities=21%  Similarity=0.228  Sum_probs=72.6

Q ss_pred             CCCceEEEecCCCC-CCCc-eeEeeeCC-eeeEeecCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHhc
Q psy9180         146 YANYTICYTDGSKT-MNTT-SCAFSIDD-LISSSQLNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSN  222 (491)
Q Consensus       146 ~~~~i~IyTDGS~~-~~~v-G~g~v~~~-~~~~~~l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~~  222 (491)
                      .++..++|||||+. +++. |+|++..+ ......+ ..+|++.|||.||++||+..    ..++.|+|||+++++++.+
T Consensus         5 i~~~~t~ytDGs~~~n~~~g~~g~~~~~~~~~~~~~-~~~TNn~aEl~Avi~aL~~~----~~~v~I~TDS~yvi~~i~~   79 (110)
T d1s1ta1           5 IVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTL-TDTTNQKTELQAIYLALQDS----GLEVNIVTDSQYALGIIQA   79 (110)
T ss_dssp             CTTSEEEEEEEEEETTTTEEEEEEEETTSCEEEEEE-SSCCHHHHHHHHHHHHHHHS----CSEEEEEECCHHHHHHHHH
T ss_pred             CCCCcEEEEeCCCCCCCCCcEEEEEEecCCeEEEec-ccCcHHHHHHHHHHHHHHhC----CCeEEEEEehHHHHHHHhc
Confidence            45667899999976 4443 44444432 2333333 46799999999999999853    5689999999999999998


Q ss_pred             ccCCCCCcchhHHHHH-HhhcCCCeEEEEEeecc
Q psy9180         223 VSFTNPLVSKVYSCWD-LLRSRNKVVHFLWCPSH  255 (491)
Q Consensus       223 ~~~~~~~~~~~~~~~I-~l~~~~~~V~~~WVPgH  255 (491)
                      +...+.   +...++| ........|.+.|||||
T Consensus        80 ~~~~~~---~~l~~~il~~l~~~~~v~i~WVpgH  110 (110)
T d1s1ta1          80 QPDQSE---SELVNQIIEQLIKKEKVYLAWVPAH  110 (110)
T ss_dssp             CCSEES---CHHHHHHHHHHHHCSEEEEEECCSS
T ss_pred             Cccccc---hHHHHHHHHHHhcCCceEEEEeCCC
Confidence            764332   3445555 22233578999999999

>d1zbfa1 c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: Ribonuclease H-like
family: Ribonuclease H
domain: BH0863-like Ribonuclease H
species: Bacillus halodurans [TaxId: 86665]

Probab=99.33  E-value=1.4e-13  Score=119.40  Aligned_cols=114  Identities=11%  Similarity=-0.063  Sum_probs=81.2

Q ss_pred             EEEecCCCCC--CCceeEeeeCC--eeeEee-cCCCccchHHHHHHHHHHHHHHHcCCCCeEEEEcccHHHHHHHhcccC
Q psy9180         151 ICYTDGSKTM--NTTSCAFSIDD--LISSSQ-LNPVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSNVSF  225 (491)
Q Consensus       151 ~IyTDGS~~~--~~vG~g~v~~~--~~~~~~-l~~~~sv~~AEl~AI~~AL~~~~~~~~~~i~I~tDSqsal~aL~~~~~  225 (491)
                      .||||||+..  |..|+|+|+..  ....++ .-..+|++.||++|++.||+.+.+.+ .++.|+|||++|+..+.++..
T Consensus         6 sIy~DGa~~GNPGp~g~g~v~~~~~~~~~~sg~~~~~TNN~aEl~A~i~aL~~~~~~~-~~i~I~tDS~yvi~wv~~~~~   84 (132)
T d1zbfa1           6 SLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERN-SRKPIYSNSQTAIKWVKDKKA   84 (132)
T ss_dssp             SEEEEEEECSSSEEEEEEEEETTTCCEEEECCCEEEECHHHHHHHHHHHHHHHHHHTT-CCCCEEESCHHHHHHHHHTCC
T ss_pred             eEEEeecCCCCCchheEEEEEEcCCEEEEEEcCcCccchHHHHHHHHHHHHHHhhcCC-ceEEEEeccHHHHHHHHhCce
Confidence            4899999983  45788877532  222222 12467899999999999999998754 579999999999999987653


Q ss_pred             CC----CCcchhHHHHH-H--hhcCCCeEEEEEeeccCCCCCChHHh
Q psy9180         226 TN----PLVSKVYSCWD-L--LRSRNKVVHFLWCPSHCGIRGNEAVD  265 (491)
Q Consensus       226 ~~----~~~~~~~~~~I-~--l~~~~~~V~~~WVPgH~gi~gNE~AD  265 (491)
                      +.    +...+++.+.+ .  .-.+...+.+.|++.|++.-||..||
T Consensus        85 kt~~~~~vkN~~l~~~i~~a~~~lk~h~~~~~~~KW~~~~wG~i~AD  131 (132)
T d1zbfa1          85 KSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKWQTDKWGEIKAD  131 (132)
T ss_dssp             CCCCCCSTTTHHHHHHHHHHHHHHHHCCCCCCEEECCHHHHCSCTTC
T ss_pred             ecCcCCCcccHHHHHHHHHHHHHHHhCCcCceeEEecCcccccCCCC
Confidence            21    11223444444 1  11345668999999999999999998